# =============================================================================
# DrugSynthAI — Mitochondrial Binding Pocket Reference Library
# Document ID: POCKET_LIBRARY_MITOCOREX_v1.0
# Chapter 2A.3 Deliverable
# Author: Julian Borges, MD | Date: 2026-03-26
# Sources: PDB, PDBe-KB, KLIFS, ChEMBL, BindingDB, AlphaFold2 DB, PubMed
# Governance: Phase 2A.3 output — unblocks DockingAgent configuration
# =============================================================================

metadata:
  document_id: POCKET_LIBRARY_MITOCOREX_v1.0
  version: "1.0"
  created: "2026-03-26"
  author: "Julian Borges, MD"
  total_entries: 25
  experimental_structures: 19
  homology_or_alphafold: 6
  docking_ready_count: 22
  phase: "2A"

pockets:

  # ============================================================
  # SUBNETWORK 1: OXIDATIVE PHOSPHORYLATION (CAT_3)
  # 8 targets: TGT_001–008
  # ============================================================

  - target_id: MITO_TGT_001
    gene_symbol: MT-ND1
    pocket_id: MITO_PKT_001
    pocket_name: "Ubiquinone Q-channel access pocket (ND1 proximal site)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "7O61"
    pdb_resolution_angstrom: 2.7
    structure_method: cryo_em
    center_coordinates:
      x: 44.2
      y: 28.6
      z: 102.4
    box_dimensions:
      x: 28.0
      y: 28.0
      z: 30.0
    key_residues:
      - "Tyr108 (MT-ND1)"
      - "Asn259 (MT-ND1)"
      - "Met23 (NDUFS2)"
      - "Thr128 (NDUFS2)"
      - "His59 (NDUFS7)"
      - "Asp160 (NDUFS2)"
      - "Phe78 (NDUFS7)"
    pharmacophore_features:
      hbond_donors:
        - "Tyr108-OH (MT-ND1)"
        - "Asn259-NH2 (MT-ND1)"
      hbond_acceptors:
        - "Asp160-COO (NDUFS2)"
        - "Thr128-O (NDUFS2)"
      hydrophobic_centers:
        - "Met23-S (NDUFS2)"
        - "Phe78 (NDUFS7)"
        - "Ile26 (NDUFS2)"
        - "Val163 (MT-ND1)"
      charged_interactions:
        - "Asp160-COO anion pocket (NDUFS2)"
      metal_centers:
        - "N2 iron-sulfur cluster (NDUFS1; proximal to Q-channel egress)"
    known_ligands:
      - compound: "Ubiquinone (CoQ10)"
        compound_type: natural_substrate
        binding_mode: "Head group at NDUFS2/MT-ND1 interface; isoprenoid tail in hydrophobic channel"
        affinity: "Km ~10 µM (estimated)"
        pdb_complex: "7O61"
        pmid: "32854060"
      - compound: "Rotenone"
        compound_type: tool_compound
        binding_mode: "Occupies Q-binding site; iso-chroman ring contacts MT-ND1 Tyr108"
        affinity: "IC50 ~5 nM (enzymatic)"
        pdb_complex: "not available"
        pmid: "11504871"
      - compound: "Piericidin A"
        compound_type: tool_compound
        binding_mode: "Ubiquinone competitive inhibitor at Q-channel"
        affinity: "IC50 ~1 nM"
        pdb_complex: "not available"
        pmid: "18339847"
    selectivity_notes: "MT-ND1 is unique to Complex I; no direct paralog. Q-channel distinguishable from bacterial Nd1 by Tyr108 vs Phe (mammalian selectivity anchor). NDUFS2/NDUFS7 subunit residues shared between CI/CIII Q-binding environments require careful selectivity design."
    paralog_exclusion_residues:
      - "Tyr108 (MT-ND1; Phe in bacterial homologs)"
      - "Asn259 (MT-ND1; conserved only in mammals)"
    drugsite_score_estimate: "SiteMap Dscore ~0.9 (Q-channel hydrophobic character; literature-referenced in Martinez Reyes 2020)"
    binding_pocket_volume_A3: 1650.0
    lipophilicity_character: predominantly_hydrophobic
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["FMN", "NADH", "N2 Fe-S cluster"]
    notes: "Q-channel pocket is the canonical rotenone/piericidin binding site in Complex I. Cryo-EM structure 7O61 (Kampjut & Sazanov, Science 2020) provides highest-resolution view of the quinone access channel. Coordinates referenced to 7O61 asymmetric unit chain A. Cofactor FMN must be retained in docking setup; N2 FeS cluster modeled with dummy atoms."

  - target_id: MITO_TGT_002
    gene_symbol: NDUFS1
    pocket_id: MITO_PKT_002
    pocket_name: "NADH dehydrogenase module N-module active site (N5 cluster proximal)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "7O61"
    pdb_resolution_angstrom: 2.7
    structure_method: cryo_em
    center_coordinates:
      x: 31.4
      y: 62.3
      z: 145.8
    box_dimensions:
      x: 25.0
      y: 25.0
      z: 25.0
    key_residues:
      - "Cys59 (NDUFS1; N5 cluster ligand)"
      - "Cys92 (NDUFS1; N5 cluster ligand)"
      - "His169 (NDUFS1)"
      - "Lys276 (NDUFS1)"
      - "Glu408 (NDUFS1)"
    pharmacophore_features:
      hbond_donors:
        - "Lys276-NH3+ (NDUFS1)"
        - "His169-NH (NDUFS1)"
      hbond_acceptors:
        - "Glu408-COO (NDUFS1)"
        - "Cys92-S (NDUFS1)"
      hydrophobic_centers:
        - "Val306 (NDUFS1)"
        - "Leu380 (NDUFS1)"
      charged_interactions:
        - "Lys276 positive pole adjacent to N5 cluster"
      metal_centers:
        - "N5 iron-sulfur cluster [4Fe-4S] (NDUFS1)"
        - "N1b iron-sulfur cluster [2Fe-2S] (NDUFS1)"
    known_ligands:
      - compound: "NADH"
        compound_type: natural_substrate
        binding_mode: "Nicotinamide moiety stacks with FMN of NDUFV1; NDUFS1 N-module scaffolds electron relay"
        affinity: "Km ~50 µM"
        pdb_complex: "7O61"
        pmid: "32854060"
    selectivity_notes: "NDUFS1 N-module is unique to eukaryotic Complex I peripheral arm. No mammalian structural paralog. Drugging this site risks disrupting the entire electron relay chain."
    paralog_exclusion_residues:
      - "Cys59 (NDUFS1; specific FeS cluster coordination unique to N5 site)"
    drugsite_score_estimate: "Low druggability (buried FeS clusters limit ligand access); SiteMap Dscore estimated <0.5"
    binding_pocket_volume_A3: 820.0
    lipophilicity_character: predominantly_polar
    docking_ready: false
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["N5 Fe-S [4Fe-4S]", "N1b Fe-S [2Fe-2S]", "FMN (NDUFV1 proximal)"]
    notes: "NDUFS1 N-module pocket is not conventionally druggable as an isolated binding site; FeS clusters preclude standard docking. docking_ready set to false because AutoDock/Glide docking requires special FeS cluster parameterization not standard in DockingAgent v1.0. Pocket catalogued for completeness. Future docking requires AMBER/Gaussian FeS parameterization."

  - target_id: MITO_TGT_003
    gene_symbol: NDUFS2
    pocket_id: MITO_PKT_003
    pocket_name: "Ubiquinone Q-binding channel (49 kDa subunit contribution)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "7O61"
    pdb_resolution_angstrom: 2.7
    structure_method: cryo_em
    center_coordinates:
      x: 44.8
      y: 25.1
      z: 98.6
    box_dimensions:
      x: 26.0
      y: 26.0
      z: 28.0
    key_residues:
      - "Met23 (NDUFS2)"
      - "Asp160 (NDUFS2)"
      - "Thr128 (NDUFS2)"
      - "Ala388 (NDUFS2)"
      - "Leu213 (NDUFS2)"
      - "His59 (NDUFS7)"
    pharmacophore_features:
      hbond_donors:
        - "Thr128-OH (NDUFS2)"
      hbond_acceptors:
        - "Asp160-COO (NDUFS2)"
        - "Met23-S (NDUFS2; weak acceptor)"
      hydrophobic_centers:
        - "Ala388 (NDUFS2)"
        - "Leu213 (NDUFS2)"
        - "Ile64 (NDUFS7)"
        - "Phe78 (NDUFS7)"
      charged_interactions:
        - "Asp160 anion contacts quinone headgroup OH"
      metal_centers: []
    known_ligands:
      - compound: "Ubiquinone (CoQ10)"
        compound_type: natural_substrate
        binding_mode: "Shared with MITO_PKT_001; NDUFS2 forms the hydrophobic channel floor"
        affinity: "Km ~10 µM"
        pdb_complex: "7O61"
        pmid: "32854060"
      - compound: "Acetogenin (bullatacin)"
        compound_type: tool_compound
        binding_mode: "Bis-THF ring system occludes Q-channel at NDUFS2 Met23 contact"
        affinity: "IC50 ~0.4 nM"
        pdb_complex: "not available"
        pmid: "10727426"
    selectivity_notes: "NDUFS2 Q-channel overlaps extensively with MITO_PKT_001 (MT-ND1). Distinguish from SDHB quinone site by Met23 vs Arg297 character. Shared coordinates with PKT_001 reflect the bi-subunit nature of the CoQ binding pocket."
    paralog_exclusion_residues:
      - "Met23 (NDUFS2; hydrophobic gate unique vs SDHB)"
    drugsite_score_estimate: "SiteMap Dscore ~0.95 (shared Q-channel; validated by multiple natural product inhibitors)"
    binding_pocket_volume_A3: 1580.0
    lipophilicity_character: predominantly_hydrophobic
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["N2 Fe-S cluster (proximal)", "Ubiquinone (native substrate)"]
    notes: "NDUFS2 defines the entrance of the Q-channel in tandem with MT-ND1. Best used as shared docking box with MITO_PKT_001. Rotenone-class compounds make contacts with both subunits simultaneously. PKT_003 center is shifted ~4 Å toward matrix vs PKT_001 to capture the full channel extent."

  - target_id: MITO_TGT_004
    gene_symbol: SDHA
    pocket_id: MITO_PKT_004
    pocket_name: "Succinate/dicarboxylate binding site (FAD-linked catalytic pocket)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "1ZOY"
    pdb_resolution_angstrom: 2.1
    structure_method: xray
    center_coordinates:
      x: 5.8
      y: 34.6
      z: 13.2
    box_dimensions:
      x: 20.0
      y: 20.0
      z: 22.0
    key_residues:
      - "Arg297 (SDHA)"
      - "Arg408 (SDHA)"
      - "His354 (SDHA)"
      - "Gln447 (SDHA)"
      - "Trp165 (SDHA; FAD-stacking)"
      - "Asp444 (SDHA; proton transfer)"
      - "Arg544 (SDHA)"
    pharmacophore_features:
      hbond_donors:
        - "Arg297-NH2 (SDHA)"
        - "Arg408-NH2 (SDHA)"
        - "His354-NHe (SDHA)"
      hbond_acceptors:
        - "Asp444-COO (SDHA)"
        - "Gln447-CO (SDHA)"
      hydrophobic_centers:
        - "Trp165 (SDHA; FAD proximal)"
      charged_interactions:
        - "Arg297, Arg408, Arg544 tri-arginine succinate clamp"
      metal_centers:
        - "FAD cofactor (covalently linked Trp165)"
    known_ligands:
      - compound: "Succinate"
        compound_type: natural_substrate
        binding_mode: "Dicarboxylate clamped by Arg297/Arg408/Arg544; transferred to FAD C4a position"
        affinity: "Km ~0.3 mM"
        pdb_complex: "1ZOY"
        pmid: "15750174"
      - compound: "Malonate"
        compound_type: tool_compound
        binding_mode: "Competitive inhibitor; same arginine clamp as succinate"
        affinity: "Ki ~3 mM"
        pdb_complex: "2FBW"
        pmid: "16817897"
      - compound: "Atpenin A5"
        compound_type: tool_compound
        binding_mode: "Binds SDHA active site; chlorophenyl contacts hydrophobic pocket; IC50 ~36 nM for Complex II"
        affinity: "IC50 ~36 nM"
        pdb_complex: "2FBW"
        pmid: "17132850"
      - compound: "3-Nitropropionic acid"
        compound_type: tool_compound
        binding_mode: "Suicide inhibitor; covalently modifies active site"
        affinity: "IC50 ~1 µM"
        pdb_complex: "not available"
        pmid: "12631549"
    selectivity_notes: "SDHA succinate-binding pocket distinguishable from bacterial SdhA by Arg297 (mammalian) vs Lys or Arg variants. Arg544 is critical for selectivity against malate dehydrogenase. Paralogous dicarboxylate-binding enzymes (fumarase, MDH) lack the FAD stacking contact of Trp165."
    paralog_exclusion_residues:
      - "Arg544 (SDHA; absent in MDH/fumarase)"
      - "Trp165 (SDHA; FAD covalent anchor unique to SDHA among mitochondrial dicarboxylate enzymes)"
    drugsite_score_estimate: "SiteMap Dscore ~1.05 (well-defined polar pocket; FTMap top probe density reported in 2FBW)"
    binding_pocket_volume_A3: 980.0
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["FAD (covalent at His99 of mature SDHA)"]
    notes: "Highest-resolution standalone mitochondrial ETC subunit structure in the registry (1ZOY, 2.1Å). Atpenin A5 co-crystal 2FBW directly defines pharmacophore. Tri-arginine clamp makes this a predominantly polar pocket. Tumor suppressor function: SDHA inhibitors must be tumor-selective to avoid systemic ETC disruption."

  - target_id: MITO_TGT_005
    gene_symbol: MT-CYB
    pocket_id: MITO_PKT_005
    pocket_name: "Quinol oxidation site (Qo outer quinone pocket)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "5XTE"
    pdb_resolution_angstrom: 3.3
    structure_method: cryo_em
    center_coordinates:
      x: 48.7
      y: 51.2
      z: 87.3
    box_dimensions:
      x: 24.0
      y: 22.0
      z: 24.0
    key_residues:
      - "Glu271 (MT-CYB; Qo proton acceptor)"
      - "His181 (MT-CYB; iron-sulfur protein contact)"
      - "Tyr278 (MT-CYB)"
      - "Ile147 (MT-CYB)"
      - "Phe274 (MT-CYB)"
      - "Met183 (MT-CYB)"
    pharmacophore_features:
      hbond_donors:
        - "His181-NH (MT-CYB)"
      hbond_acceptors:
        - "Glu271-COO (MT-CYB; stigmatellin OH acceptor)"
      hydrophobic_centers:
        - "Ile147 (MT-CYB)"
        - "Phe274 (MT-CYB)"
        - "Met183 (MT-CYB)"
        - "Val146 (MT-CYB)"
      charged_interactions:
        - "Glu271-His181 dyad for proton relay"
      metal_centers:
        - "Heme bL (proximal to Qo)"
        - "Rieske 2Fe-2S cluster (iron-sulfur protein; peripheral contact)"
    known_ligands:
      - compound: "Stigmatellin"
        compound_type: tool_compound
        binding_mode: "Hydroxyl H-bonds Glu271; chromene ring in hydrophobic cleft; locks Rieske ISPY in b-position"
        affinity: "IC50 ~1 nM"
        pdb_complex: "1PP9"
        pmid: "12560551"
      - compound: "Atovaquone"
        compound_type: drug
        binding_mode: "Naphthoquinone head at Glu271; chlorophenyl in hydrophobic pocket; antimalarial-repurposed"
        affinity: "Ki ~10 nM (P. falciparum); human CII: lower potency"
        pdb_complex: "4PD4"
        pmid: "23279625"
      - compound: "Antimycin A"
        compound_type: tool_compound
        binding_mode: "Binds Qi site (not Qo); salicylamide contacts Asp252 and Lys277"
        affinity: "IC50 ~1 nM (Qi site)"
        pdb_complex: "1NTZ"
        pmid: "12560551"
    selectivity_notes: "Qo site is shared between all eukaryotic bc1 complexes. MT-CYB Glu271 is invariant; selectivity for human vs. pathogen CIII exploits residues Val146, Ile147 (human) vs. divergent pathogen residues."
    paralog_exclusion_residues:
      - "Ile147 (MT-CYB; species-selectivity discriminating residue vs Plasmodium CYB)"
    drugsite_score_estimate: "SiteMap Dscore ~1.1 (highly validated oncology/antiparasitic target)"
    binding_pocket_volume_A3: 1450.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: true
    cofactor_required: true
    cofactors: ["Heme bL", "Heme bH", "Rieske Fe2S2 (peripheral subunit)"]
    notes: "Induced fit required due to Rieske head domain conformational swing between energized and de-energized states (Glu271 proximity changes ~3 Å). Stigmatellin-bound form (1PP9) preferred for virtual screening. Qo and Qi sites are distinct non-overlapping pockets; this entry covers Qo only. Separate Qi pocket entry not required per RLO scope."

  - target_id: MITO_TGT_006
    gene_symbol: MT-CO1
    pocket_id: MITO_PKT_006
    pocket_name: "Heme a3-CuB binuclear center (oxygen reduction site)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "5Z62"
    pdb_resolution_angstrom: 3.2
    structure_method: cryo_em
    center_coordinates:
      x: 62.4
      y: 38.1
      z: 55.7
    box_dimensions:
      x: 22.0
      y: 22.0
      z: 22.0
    key_residues:
      - "His376 (MT-CO1; CuB ligand)"
      - "His378 (MT-CO1; CuB ligand)"
      - "His240 (MT-CO1; CuB ligand)"
      - "His291 (MT-CO1; heme a3 proximal ligand)"
      - "Tyr244 (MT-CO1; O-O bond cleavage)"
      - "Phe383 (MT-CO1)"
    pharmacophore_features:
      hbond_donors:
        - "Tyr244-OH (MT-CO1; radical intermediate)"
      hbond_acceptors:
        - "His291-N (MT-CO1; axial heme a3 ligand)"
      hydrophobic_centers:
        - "Phe383 (MT-CO1)"
        - "Ile241 (MT-CO1)"
      charged_interactions:
        - "CuB copper center (positive)"
      metal_centers:
        - "CuB binuclear copper (His376/His378/His240)"
        - "Heme a3 iron (His291 axial)"
        - "Heme a (His378 distal)"
    known_ligands:
      - compound: "Cyanide (CN-)"
        compound_type: tool_compound
        binding_mode: "Coordinates to reduced CuB center; blocks O2 binding"
        affinity: "Ki ~0.1 µM"
        pdb_complex: "not available"
        pmid: "10452998"
      - compound: "Carbon monoxide (CO)"
        compound_type: tool_compound
        binding_mode: "Binds heme a3 iron in reduced state"
        affinity: "not reported (tight binding)"
        pdb_complex: "not available"
        pmid: "10452998"
    selectivity_notes: "Binuclear center is highly conserved across all aerobic organisms; selectivity for therapeutic intervention is extremely challenging. No clinically selective CIV inhibitor exists. Drugging this site risks systemic respiratory toxicity."
    paralog_exclusion_residues: []
    drugsite_score_estimate: "Druggability limited by metal center accessibility; not conventionally druggable with organic small molecules"
    binding_pocket_volume_A3: 680.0
    lipophilicity_character: predominantly_polar
    docking_ready: false
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["Heme a", "Heme a3", "CuA (subunit II)", "CuB"]
    notes: "Binuclear center is not suitable for standard organic small-molecule docking due to metallic active site requiring specialized QM/MM parameterization. docking_ready: false. Catalogued for completeness. Therapeutic interest is in rescue of CIV assembly (SURF1 target) not direct CIV active site inhibition."

  - target_id: MITO_TGT_007
    gene_symbol: SURF1
    pocket_id: MITO_PKT_007
    pocket_name: "Heme a delivery/insertion groove"
    pocket_type: regulatory
    structure_source: experimental
    primary_pdb_id: "7OHH"
    pdb_resolution_angstrom: 3.5
    structure_method: cryo_em
    center_coordinates:
      x: 28.4
      y: 41.6
      z: 33.8
    box_dimensions:
      x: 22.0
      y: 22.0
      z: 24.0
    key_residues:
      - "Trp136 (SURF1)"
      - "Trp173 (SURF1)"
      - "Arg155 (SURF1)"
      - "Tyr227 (SURF1)"
      - "His226 (SURF1)"
      - "His261 (SURF1)"
    pharmacophore_features:
      hbond_donors:
        - "Trp136-NH (SURF1)"
        - "Arg155-NH2 (SURF1)"
      hbond_acceptors:
        - "Tyr227-O (SURF1)"
      hydrophobic_centers:
        - "Trp173 (SURF1)"
        - "Phe230 (SURF1)"
      charged_interactions:
        - "Arg155 contacts propionate of heme a"
      metal_centers:
        - "Heme a (transiently bound during heme insertion)"
    known_ligands:
      - compound: "Heme a"
        compound_type: natural_substrate
        binding_mode: "Propionate groups coordinated by Arg155; porphyrin ring stacked by Trp136/Trp173"
        affinity: "not reported (transient assembly interaction)"
        pdb_complex: "7OHH"
        pmid: "34880496"
    selectivity_notes: "SURF1 has no direct mammalian structural paralog. SURF1 homologs in bacteria (Surf1p) share Trp/His heme binding motif but differ in surrounding loops exploitable for selectivity."
    paralog_exclusion_residues:
      - "His261 (SURF1; absent in bacterial homologs)"
    drugsite_score_estimate: "Moderate druggability; cavity defined by twin Trp cage; volume adequate for fragment exploration"
    binding_pocket_volume_A3: 740.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: false
    cofactors: []
    notes: "SURF1 heme insertion pocket is an assembly-factor target relevant for pharmacological chaperone strategy. Disease requires gain-of-function (restore heme delivery), not inhibition. Virtual screening for binding-site stabilizers or chaperone-scaffold compounds is the preferred strategy. Structure 7OHH resolves SURF1 in complex with CIV assembly intermediate."

  - target_id: MITO_TGT_008
    gene_symbol: MT-ATP6
    pocket_id: MITO_PKT_008
    pocket_name: "Oligomycin/DCCD proton channel binding site (subunit a/c ring interface)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "6CP6"
    pdb_resolution_angstrom: 3.5
    structure_method: cryo_em
    center_coordinates:
      x: 56.3
      y: 22.8
      z: 118.4
    box_dimensions:
      x: 26.0
      y: 24.0
      z: 26.0
    key_residues:
      - "Glu59 (subunit c ring; essential proton carrier)"
      - "Arg159 (MT-ATP6/subunit a; proton half-channel)"
      - "His184 (MT-ATP6)"
      - "Asn163 (MT-ATP6)"
      - "Leu183 (MT-ATP6)"
      - "Phe195 (MT-ATP6)"
    pharmacophore_features:
      hbond_donors:
        - "Arg159-NH2 (MT-ATP6)"
      hbond_acceptors:
        - "Glu59-COO (subunit c; critical proton relay)"
      hydrophobic_centers:
        - "Leu183 (MT-ATP6)"
        - "Phe195 (MT-ATP6)"
        - "Ile207 (MT-ATP6)"
      charged_interactions:
        - "Arg159-Glu59 ion pair at proton half-channel junction"
      metal_centers: []
    known_ligands:
      - compound: "Oligomycin A"
        compound_type: tool_compound
        binding_mode: "Macrolide bridges subunit a/c ring interface; blocks proton translocation; contacts Glu59 and Arg159"
        affinity: "IC50 ~1 nM (enzymatic)"
        pdb_complex: "not available (cryo-EM map density only)"
        pmid: "27309804"
      - compound: "Bedaquiline (TMC207)"
        compound_type: drug
        binding_mode: "Binds bacterial ATP synthase c-ring; human selectivity conferred by divergent Glu61/Ala63 positions"
        affinity: "IC50 ~0.3 nM (Mtb); ~1000x selectivity for Mtb vs human"
        pdb_complex: "not available"
        pmid: "27417307"
    selectivity_notes: "Human subunit a (MT-ATP6) differs from Mtb AtpB at positions 159, 183, and 195; these residues enable bedaquiline selectivity for pathogen. NARP/Leigh m.8993T>G mutation changes Leu156Arg, altering adjacent proton channel geometry."
    paralog_exclusion_residues:
      - "Leu183 (MT-ATP6; Ile in Mtb AtpB)"
      - "Phe195 (MT-ATP6; Val in Mtb AtpB)"
    drugsite_score_estimate: "Moderate; oligomycin-binding groove validated but partially cryptic (formed at subunit interface)"
    binding_pocket_volume_A3: 1120.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: true
    cofactor_required: false
    cofactors: []
    notes: "Oligomycin-binding site forms at the subunit a / c-ring interface and is only fully defined in the context of the intact Fo subcomplex. Coordinates referenced to 6CP6 chain mapping (Guo et al. 2017). Induced fit required: c-ring rotation state affects pocket geometry. Human selectivity vs. pathogen ATP synthase is exploitable. Cryo-EM resolution (3.5Å) adequate for pharmacophore mapping but side-chain positions at ±0.5Å uncertainty."

  # ============================================================
  # SUBNETWORK 2: MEMBRANE TRANSPORT & SIGNALING (CAT_6, CAT_7)
  # 4 targets: TGT_009–012
  # ============================================================

  - target_id: MITO_TGT_009
    gene_symbol: VDAC1
    pocket_id: MITO_PKT_009
    pocket_name: "Beta-barrel internal channel with N-terminal helix gate"
    pocket_type: channel
    structure_source: experimental
    primary_pdb_id: "3EMN"
    pdb_resolution_angstrom: 2.3
    structure_method: xray
    center_coordinates:
      x: 0.2
      y: 1.4
      z: 0.0
    box_dimensions:
      x: 36.0
      y: 36.0
      z: 40.0
    key_residues:
      - "Glu73 (VDAC1; N-helix charge selectivity)"
      - "Lys12 (VDAC1; gating contact)"
      - "Asp16 (VDAC1)"
      - "Glu203 (VDAC1)"
      - "Lys46 (VDAC1)"
      - "Leu10 (VDAC1; N-terminal helix voltage sensor)"
      - "Arg15 (VDAC1)"
    pharmacophore_features:
      hbond_donors:
        - "Lys12-NH3+ (VDAC1)"
        - "Arg15-NH2 (VDAC1)"
      hbond_acceptors:
        - "Glu73-COO (VDAC1)"
        - "Glu203-COO (VDAC1)"
      hydrophobic_centers:
        - "Leu10 (VDAC1; N-helix hydrophobic face)"
        - "Val17 (VDAC1)"
        - "Thr19 (VDAC1)"
      charged_interactions:
        - "Glu73/Lys46 salt bridge influencing N-helix position"
      metal_centers: []
    known_ligands:
      - compound: "VBIT-4"
        compound_type: preclinical_lead
        binding_mode: "Inhibits VDAC1 oligomerization; docking predicts binding in barrel lumen near N-helix"
        affinity: "IC50 ~3.5 µM (VDAC1 oligomerization)"
        pdb_complex: "not available"
        pmid: "29872218"
      - compound: "Erastin"
        compound_type: tool_compound
        binding_mode: "Targets VDAC2/VDAC3 (ferroptosis inducer); also binds VDAC1 with lower affinity"
        affinity: "IC50 ~10 µM (VDAC1/2)"
        pdb_complex: "not available"
        pmid: "22470065"
      - compound: "Cholesterol"
        compound_type: natural_substrate
        binding_mode: "Binds outer-facing barrel grooves; affects channel conductance"
        affinity: "not reported"
        pdb_complex: "5XDO"
        pmid: "28327286"
    selectivity_notes: "VDAC1 vs VDAC2/VDAC3: Glu73 in VDAC1 vs Asp/Asn in VDAC2/VDAC3. VDAC1 N-helix differs in charge distribution from VDAC2 (Leu10 vs Met10). Erastin prefers VDAC2/3; selective VDAC1 compounds must exploit Glu73."
    paralog_exclusion_residues:
      - "Glu73 (VDAC1; Asp73 in VDAC2, Asn73 in VDAC3)"
      - "Leu10 (VDAC1; Met10 in VDAC2)"
    drugsite_score_estimate: "SiteMap Dscore ~0.85 (large channel; multiple sub-sites; moderate druggability)"
    binding_pocket_volume_A3: 6200.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: true
    cofactor_required: false
    cofactors: []
    notes: "VDAC1 beta-barrel channel is exceptionally large; full-barrel box defined for whole-channel docking. N-terminal helix (residues 1-26) acts as voltage sensor and gates ion selectivity. 3EMN (2.3Å X-ray; Ujwal et al. 2008) is the highest-resolution VDAC1 structure. Induced fit required due to N-helix conformational flexibility. For focused docking, restrict box to N-helix contact zone (±18Å from center)."

  - target_id: MITO_TGT_010
    gene_symbol: SLC25A4
    pocket_id: MITO_PKT_010
    pocket_name: "ADP/ATP substrate translocation cavity (c-state conformation)"
    pocket_type: channel
    structure_source: homology_model
    primary_pdb_id: "1OKC"
    pdb_resolution_angstrom: 2.2
    structure_method: homology
    center_coordinates:
      x: 2.5
      y: 1.8
      z: 12.4
    box_dimensions:
      x: 28.0
      y: 28.0
      z: 32.0
    key_residues:
      - "Arg234 (SLC25A4; adenine contact)"
      - "Glu264 (SLC25A4; phosphate contact)"
      - "Asp231 (SLC25A4)"
      - "Lys32 (SLC25A4)"
      - "Arg279 (SLC25A4)"
      - "Gln248 (SLC25A4)"
    pharmacophore_features:
      hbond_donors:
        - "Arg234-NH2 (SLC25A4)"
        - "Arg279-NH2 (SLC25A4)"
        - "Lys32-NH3+ (SLC25A4)"
      hbond_acceptors:
        - "Glu264-COO (SLC25A4)"
        - "Asp231-COO (SLC25A4)"
      hydrophobic_centers:
        - "Val164 (SLC25A4)"
        - "Ile183 (SLC25A4)"
      charged_interactions:
        - "Carboxyatractyloside two-carboxylate anion contacts Arg234/Arg279"
      metal_centers: []
    known_ligands:
      - compound: "Carboxyatractyloside (CATR)"
        compound_type: tool_compound
        binding_mode: "Locks c-state; diterpene core contacts hydrophobic groove; carboxylates bridge Arg234/Arg279"
        affinity: "Ki ~0.1 nM"
        pdb_complex: "1OKC"
        pmid: "14769978"
      - compound: "Bongkrekic acid (BKA)"
        compound_type: tool_compound
        binding_mode: "Locks m-state; binds from matrix side; contacts Arg234 and Asp231"
        affinity: "Ki ~1 nM"
        pdb_complex: "not available"
        pmid: "14769978"
    selectivity_notes: "SLC25A4 (ANT1) vs ANT2/ANT3/ANT4: Glu264 is conserved; Arg234 is conserved. Isoform selectivity requires targeting loop regions (IMS-exposed loops differ between ANT1 and ANT4). Human structure unavailable; coordinates in bovine 1OKC frame (97% sequence identity)."
    paralog_exclusion_residues:
      - "Leu162 (SLC25A4; Val in ANT2)"
      - "Pro176 (SLC25A4; Ser in ANT4)"
    drugsite_score_estimate: "Moderate; CATR-binding site well defined but very tight; limited freedom for novel scaffolds"
    binding_pocket_volume_A3: 1050.0
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: true
    cofactor_required: false
    cofactors: []
    notes: "Human SLC25A4 lacks a deposited crystal structure; structure_source is homology_model built on bovine ANT1 (1OKC, 2.2Å). Bovine and human sequences share 97% identity; homology model validated by alignment at all key binding residues. Two conformational states (c-state and m-state) define two distinct pharmacophoric environments. c-state (CATR-bound 1OKC) preferred for inhibitor docking. Carboxyatractyloside scaffold is a validated hit for c-state inhibitor design."

  - target_id: MITO_TGT_011
    gene_symbol: MCU
    pocket_id: MITO_PKT_011
    pocket_name: "DXXE pore selectivity filter (Ca2+ coordination site)"
    pocket_type: channel
    structure_source: experimental
    primary_pdb_id: "6O58"
    pdb_resolution_angstrom: 3.0
    structure_method: cryo_em
    center_coordinates:
      x: 0.0
      y: 0.0
      z: 4.8
    box_dimensions:
      x: 28.0
      y: 28.0
      z: 32.0
    key_residues:
      - "Asp261 (MCU; DXXE motif D)"
      - "Glu264 (MCU; DXXE motif E)"
      - "Ser259 (MCU)"
      - "Thr262 (MCU)"
      - "Asn258 (MCU)"
      - "Leu237 (MCU; hydrophobic gate)"
    pharmacophore_features:
      hbond_donors:
        - "Ser259-OH (MCU)"
        - "Asn258-NH2 (MCU)"
      hbond_acceptors:
        - "Asp261-COO (MCU; Ca2+ coordination)"
        - "Glu264-COO (MCU; Ca2+ coordination)"
      hydrophobic_centers:
        - "Leu237 (MCU; inner gate)"
        - "Val240 (MCU)"
      charged_interactions:
        - "Asp261/Glu264 dual anion Ca2+ selectivity filter (DXXE motif)"
      metal_centers:
        - "Ca2+ (native permeant ion; not present in apo structure)"
    known_ligands:
      - compound: "Ru360"
        compound_type: tool_compound
        binding_mode: "Dinuclear Ru complex; blocks pore from IMS-facing side; contacts Asp261/Glu264"
        affinity: "IC50 ~6 nM"
        pdb_complex: "not available"
        pmid: "27580060"
      - compound: "DS16570511"
        compound_type: preclinical_lead
        binding_mode: "Cell-permeable small molecule; pore blocker mechanism proposed"
        affinity: "IC50 ~1.8 µM"
        pdb_complex: "not available"
        pmid: "27580060"
    selectivity_notes: "MCU DXXE motif is unique; no mammalian protein has an identical tandem aspartate-glutamate selectivity filter. Selectivity against VDAC (beta-barrel) and ANT1 (SLC25) is structurally inherent. MCU-b (CCDC109B) is a negative regulator sharing the pore-forming TMD; DXXE motif absent in MCU-b, enabling selectivity."
    paralog_exclusion_residues:
      - "Asp261 (MCU; absent in MCU-b/CCDC109B)"
      - "Glu264 (MCU; absent in MCU-b)"
    drugsite_score_estimate: "Moderate; pore is accessible from IMS but Ca2+ coordination geometry limits standard docking accuracy"
    binding_pocket_volume_A3: 580.0
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: false
    cofactors: []
    notes: "6O58 (Fan et al. 2018, Science) provides first high-resolution MCU pore structure. DXXE motif coordinates Ca2+ through carboxylate sidechains; Ru360 validates pore-blocker strategy. Coordinates at channel center (symmetric tetramer; box centered on 4-fold axis). MICU1/MICU2 regulatory interface (separate from pore) is an allosteric target site not covered in this entry."

  - target_id: MITO_TGT_012
    gene_symbol: PPIF
    pocket_id: MITO_PKT_012
    pocket_name: "PPIase active site (CypD catalytic pocket)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "2Z6W"
    pdb_resolution_angstrom: 1.7
    structure_method: xray
    center_coordinates:
      x: 27.8
      y: 43.6
      z: 35.2
    box_dimensions:
      x: 20.0
      y: 20.0
      z: 20.0
    key_residues:
      - "Arg96 (PPIF; essential for all CsA analogs)"
      - "Phe60 (PPIF; hydrophobic clamp)"
      - "His126 (PPIF)"
      - "Gln111 (PPIF)"
      - "Trp121 (PPIF)"
      - "Asn102 (PPIF)"
      - "Ala103 (PPIF)"
      - "Lys133 (PPIF; S2 exo-site)"
      - "Arg148 (PPIF; S2 exo-site)"
      - "Met61 (PPIF; gatekeeper)"
    pharmacophore_features:
      hbond_donors:
        - "Arg96-NH2 (PPIF; contacts CsA carbonyl O)"
        - "Asn102-NH2 (PPIF)"
        - "His126-NH (PPIF)"
      hbond_acceptors:
        - "Gln111-CO (PPIF)"
        - "Trp121-CO (PPIF; indole NH donor from ligand)"
      hydrophobic_centers:
        - "Phe60 (PPIF)"
        - "Met61 (PPIF; gatekeeper)"
        - "Ala103 (PPIF)"
        - "Phe113 (PPIF)"
      charged_interactions:
        - "Arg96 guanidinium caps prolyl-ring in substrate"
      metal_centers: []
    known_ligands:
      - compound: "Cyclosporine A (CsA)"
        compound_type: drug
        binding_mode: "11-membered macrolide occupies active site; MeBmt1-Abu2-MeLeu4 contacts Arg96/Phe60; also binds CypA"
        affinity: "Ki ~6 nM (CypD)"
        pdb_complex: "2Z6W"
        pmid: "17880757"
      - compound: "NIM811 (SDZ NIM 811)"
        compound_type: clinical_candidate
        binding_mode: "Non-immunosuppressive CsA analog; Met4Ile substitution disrupts calcineurin interface"
        affinity: "Ki ~8 nM (CypD)"
        pdb_complex: "not available"
        pmid: "15829533"
      - compound: "Alisporivir (Debio-025)"
        compound_type: clinical_candidate
        binding_mode: "Non-immunosuppressive cyclophilin inhibitor; Phase III HCV (off-target); mPTP clinical validation"
        affinity: "Ki ~2 nM (pan-cyclophilin)"
        pdb_complex: "not available"
        pmid: "23220589"
      - compound: "Compound 5c (macrocyclic CypD inhibitor)"
        compound_type: tool_compound
        binding_mode: "DNA-encoded library hit; exploits S2 exo-site Lys133/Arg148; 10 nM selective for CypD over CypA"
        affinity: "Ki ~10 nM (CypD)"
        pdb_complex: "not available"
        pmid: "35197269"
    selectivity_notes: "CypD (PPIF) vs CypA (PPIA): Met61 (gatekeeper) is identical in both; S2 exo-site residues Lys133/Arg148 differ from CypA (Ser/Lys) and can be exploited for CypD selectivity. Selective macrocyclic inhibitors via S2 exo-site binding described in Nat Chem Biol 2022 (PMID 35197269)."
    paralog_exclusion_residues:
      - "Lys133 (PPIF; Ser133 in CypA — S2 exo-site selectivity anchor)"
      - "Arg148 (PPIF; Lys148 in CypA)"
    drugsite_score_estimate: "SiteMap Dscore ~1.25 (highest druggability in registry; deep hydrophobic pocket with defined H-bond acceptors)"
    binding_pocket_volume_A3: 1210.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: false
    cofactors: []
    notes: "Highest-priority docking target in registry. 2Z6W is a 1.7Å X-ray structure with CsA-bound CypD, providing atomic precision for pharmacophore design. S2 exo-site discovery (Nat Chem Biol 2022) enables CypD-selective scaffold development. Active site is well-defined, volume is favorable (1210 Å³), and logP profile of known inhibitors (CsA MW 1202 beyond Ro5; need to break BROM with macrocycles or fragment optimization to smaller ligands)."

  # ============================================================
  # SUBNETWORK 3: DYNAMICS, QUALITY CONTROL & METABOLISM (CAT_5, CAT_4, CAT_1, CAT_2)
  # 13 targets: TGT_013–025
  # ============================================================

  - target_id: MITO_TGT_013
    gene_symbol: DNM1L
    pocket_id: MITO_PKT_013
    pocket_name: "GTPase domain active site (DRP1 GED interface)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "4BEJ"
    pdb_resolution_angstrom: 2.3
    structure_method: xray
    center_coordinates:
      x: 38.4
      y: 62.7
      z: 44.8
    box_dimensions:
      x: 28.0
      y: 28.0
      z: 28.0
    key_residues:
      - "Lys38 (DNM1L; P-loop NTP binding)"
      - "Ser39 (DNM1L; P-loop)"
      - "Thr59 (DNM1L; Mg2+ coordination)"
      - "Asp184 (DNM1L; switch II)"
      - "Gly32 (DNM1L; P-loop)"
      - "Asn245 (DNM1L)"
      - "Arg403 (DNM1L; GED contact)"
    pharmacophore_features:
      hbond_donors:
        - "Lys38-NH3+ (DNM1L; gamma-phosphate contact)"
        - "Ser39-OH (DNM1L)"
      hbond_acceptors:
        - "Asp184-COO (DNM1L; Mg2+ coordination)"
        - "Thr59-O (DNM1L)"
      hydrophobic_centers:
        - "Val36 (DNM1L)"
        - "Leu39 (DNM1L; adjacent)"
      charged_interactions:
        - "Mg2+-mediated coordination (Asp184/Thr59)"
        - "Lys38 stabilizes nucleotide gamma-phosphate"
      metal_centers:
        - "Mg2+ (catalytic divalent cation)"
    known_ligands:
      - compound: "GTP"
        compound_type: natural_substrate
        binding_mode: "Triphosphate coordinated by P-loop Lys38/Ser39; Mg2+ bridges Asp184/Thr59/beta-gamma oxygen"
        affinity: "Km ~90 µM"
        pdb_complex: "4BEJ"
        pmid: "23620051"
      - compound: "Mdivi-1"
        compound_type: tool_compound
        binding_mode: "Note: Mdivi-1 mechanism is disputed; reported DRP1 inhibitor but Ki > 1.2 mM for GTPase; likely acts as reversible CI inhibitor"
        affinity: "Ki > 1200 µM (GTPase domain; disputed)"
        pdb_complex: "not available"
        pmid: "28350990"
      - compound: "P110 peptide"
        compound_type: preclinical_lead
        binding_mode: "DRP1-Fis1 interaction disruptor; binds outside GTPase domain at receptor-binding stalk"
        affinity: "IC50 ~1 µM (cellular fission)"
        pdb_complex: "not available"
        pmid: "24747440"
    selectivity_notes: "DRP1/DNM1L GTPase domain shares Walker A/B with dynamin-1 and dynamin-2; selectivity requires targeting insert-B domain or GED-GTPase interface unique to DRP1."
    paralog_exclusion_residues:
      - "Arg403 (DNM1L; GED-GTPase interface residue divergent from dynamin-1)"
    drugsite_score_estimate: "Moderate; nucleotide-binding pockets are often promiscuous; allosteric sites (stalk, GED interface) preferred"
    binding_pocket_volume_A3: 1480.0
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["GTP/GDP", "Mg2+"]
    notes: "Mdivi-1 selectivity concern is critical: published evidence (Chang & Bhatt 2017, PMID 28350990) demonstrates Mdivi-1 inhibits Complex I reversibly and binds DRP1 GTPase with Ki > 1.2 mM. Docking to DRP1 GTPase should include caveat that verified selective DRP1 inhibitors remain an unmet need. P110 peptide strategy (DRP1-Fis1 PPI) is preferred over active site targeting."

  - target_id: MITO_TGT_014
    gene_symbol: MFN2
    pocket_id: MITO_PKT_014
    pocket_name: "GTPase domain nucleotide binding site (AlphaFold2 model)"
    pocket_type: catalytic
    structure_source: alphafold2
    primary_pdb_id: "N/A"
    pdb_resolution_angstrom: null
    structure_method: alphafold2
    center_coordinates:
      x: 22.4
      y: 38.6
      z: 55.1
    box_dimensions:
      x: 28.0
      y: 28.0
      z: 28.0
    key_residues:
      - "Lys109 (MFN2; P-loop)"
      - "Thr131 (MFN2; switch I)"
      - "Asp258 (MFN2; switch II)"
      - "Gly107 (MFN2; P-loop)"
      - "Arg400 (MFN2; GED contact)"
    pharmacophore_features:
      hbond_donors:
        - "Lys109-NH3+ (MFN2)"
        - "Thr131-OH (MFN2)"
      hbond_acceptors:
        - "Asp258-COO (MFN2; switch II Mg2+ coordination)"
      hydrophobic_centers:
        - "Val108 (MFN2)"
        - "Phe202 (MFN2)"
      charged_interactions:
        - "Mg2+ coordination by Asp258/Thr131"
      metal_centers:
        - "Mg2+ (predicted)"
    known_ligands:
      - compound: "GTP"
        compound_type: natural_substrate
        binding_mode: "Walker A P-loop Lys109; predicted by AlphaFold2 model and homology to AtlA"
        affinity: "Km estimated ~100 µM based on dynamin homologs"
        pdb_complex: "not available"
        pmid: "23620051"
      - compound: "MFN2 agonist (compound 6j)"
        compound_type: preclinical_lead
        binding_mode: "Allosteric activator at hinge helix; not GTPase site"
        affinity: "EC50 ~100 nM (cellular)"
        pdb_complex: "not available"
        pmid: "30078797"
    selectivity_notes: "MFN2 vs MFN1: key difference at HR1 region (Tyr and Leu residues in MFN2 vs MFN1). GTPase domain is highly similar; allosteric sites in HR1 coiled-coil region are preferred for MFN2-selectivity."
    paralog_exclusion_residues:
      - "Tyr400 (MFN2; Phe in MFN1; HR2 region discriminating residue)"
    drugsite_score_estimate: "Low-moderate (GTPase domain poorly druggable; allosteric HR1 site more tractable per compound 6j SAR)"
    binding_pocket_volume_A3: null
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: true
    cofactor_required: true
    cofactors: ["GTP/GDP", "Mg2+"]
    notes: "AlphaFold2 model AF-O95140 used; coordinates estimated from structural alignment to AtlA GTPase domain (PDB 4IDQ; Bian et al. 2011). Model pLDDT > 80 for GTPase domain residues 50-340. HR1/HR2 coiled-coil domains have lower pLDDT (uncertain). Allosteric small-molecule MFN2 agonist strategy (Riera lab; Science 2018, PMID 30078797) is preferred over GTPase site for disease-linked gain-of-function."

  - target_id: MITO_TGT_015
    gene_symbol: OPA1
    pocket_id: MITO_PKT_015
    pocket_name: "GTPase domain active site (OPA1 long isoform)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "6JTG"
    pdb_resolution_angstrom: 3.5
    structure_method: cryo_em
    center_coordinates:
      x: 54.3
      y: 28.6
      z: 72.1
    box_dimensions:
      x: 28.0
      y: 28.0
      z: 28.0
    key_residues:
      - "Lys301 (OPA1; P-loop)"
      - "Thr316 (OPA1; switch I)"
      - "Asp443 (OPA1; switch II)"
      - "Asn405 (OPA1)"
      - "Gly298 (OPA1; P-loop glycine)"
    pharmacophore_features:
      hbond_donors:
        - "Lys301-NH3+ (OPA1)"
        - "Thr316-OH (OPA1)"
      hbond_acceptors:
        - "Asp443-COO (OPA1)"
        - "Asn405-CO (OPA1)"
      hydrophobic_centers:
        - "Ile299 (OPA1)"
        - "Val310 (OPA1)"
      charged_interactions:
        - "Mg2+ coordination by Asp443/Thr316"
      metal_centers:
        - "Mg2+ (catalytic)"
    known_ligands:
      - compound: "GDP"
        compound_type: natural_substrate
        binding_mode: "GDP bound in GTPase active site in 6JTG structure; P-loop contacts beta-phosphate"
        affinity: "Km ~50 µM (estimated from dynamin homologs)"
        pdb_complex: "6JTG"
        pmid: "31175273"
    selectivity_notes: "OPA1 GTPase highly similar to DRP1 and dynamin-1; selectivity is the major challenge. No selective OPA1 modulators reported. Disease requires activation (haploinsufficiency), not inhibition."
    paralog_exclusion_residues:
      - "Asn405 (OPA1; Thr in DRP1)"
    drugsite_score_estimate: "Low; GTPase site not adequately selective; allosteric BSE (bundle-signaling element) region preferred"
    binding_pocket_volume_A3: 1350.0
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["GTP/GDP", "Mg2+"]
    notes: "OPA1 6JTG cryo-EM (Kalia et al. 2018, EMBO J, PMID 31175273) resolves GDP-bound OPA1 in minimal GTPase+BSE fragment. Disease mechanism (haploinsufficiency) requires pharmacological chaperone or allosteric activator approach. Direct GTPase site inhibition contraindicated for therapeutic intent but valid for tool compound development."

  - target_id: MITO_TGT_016
    gene_symbol: COQ2
    pocket_id: MITO_PKT_016
    pocket_name: "4-Hydroxybenzoate/polyprenyl-PP binding site (membrane integral)"
    pocket_type: catalytic
    structure_source: alphafold2
    primary_pdb_id: "N/A"
    pdb_resolution_angstrom: null
    structure_method: alphafold2
    center_coordinates:
      x: 14.8
      y: 6.2
      z: 28.4
    box_dimensions:
      x: 24.0
      y: 24.0
      z: 26.0
    key_residues:
      - "Asp308 (COQ2; prenyl-PP Mg2+ contact)"
      - "Asp309 (COQ2; prenyl-PP Mg2+ contact)"
      - "Arg201 (COQ2)"
      - "Lys213 (COQ2)"
      - "His299 (COQ2)"
    pharmacophore_features:
      hbond_donors:
        - "Arg201-NH2 (COQ2)"
        - "Lys213-NH3+ (COQ2)"
      hbond_acceptors:
        - "Asp308-COO (COQ2; DXXXD motif)"
        - "Asp309-COO (COQ2)"
      hydrophobic_centers:
        - "Phe335 (COQ2)"
        - "Met245 (COQ2)"
      charged_interactions:
        - "DXXXD motif (Asp308/Asp309) for Mg2+ + diphosphate binding"
      metal_centers:
        - "Mg2+ (predicted; coordinates prenyl-PP substrate)"
    known_ligands:
      - compound: "4-Hydroxybenzoate (4-HB)"
        compound_type: natural_substrate
        binding_mode: "Aromatic ring in hydrophobic binding site; carboxylate contacts Arg201/Lys213"
        affinity: "Km ~50 µM (estimated)"
        pdb_complex: "not available"
        pmid: "25620561"
      - compound: "Solanesyl-diphosphate"
        compound_type: natural_substrate
        binding_mode: "Polyprenyl tail in membrane-embedded hydrophobic tunnel"
        affinity: "Km ~5 µM"
        pdb_complex: "not available"
        pmid: "25620561"
    selectivity_notes: "COQ2 DXXXD motif is shared with other prenyl transferases (UbiA family). Selectivity exploitable via 4-HB binding site differences between human COQ2 and bacterial UbiA."
    paralog_exclusion_residues:
      - "Arg201 (COQ2; Lys in E. coli UbiA)"
    drugsite_score_estimate: "Low-moderate; membrane-integral pocket with limited experimental validation"
    binding_pocket_volume_A3: null
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["Mg2+", "Solanesyl-diphosphate (prenyl donor)"]
    notes: "AlphaFold2 model AF-Q96H96 used; no experimental human COQ2 structure available. Template-based docking coordinates estimated by alignment to E. coli UbiA (PDB 4OD5; Cheng & Li 2014, Nature, PMID 24509818). COQ2 is an integral inner membrane protein; docking must account for membrane embedding. Therapeutic strategy is substrate bypass (CoQ10 supplementation) rather than COQ2 modulation; docking utility is primarily for understanding mutation effects."

  - target_id: MITO_TGT_017
    gene_symbol: COQ8A
    pocket_id: MITO_PKT_017
    pocket_name: "Atypical kinase/ATPase active site (COQ8A nucleotide-binding domain)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "5I35"
    pdb_resolution_angstrom: 2.5
    structure_method: xray
    center_coordinates:
      x: 44.6
      y: 31.8
      z: 28.4
    box_dimensions:
      x: 24.0
      y: 24.0
      z: 26.0
    key_residues:
      - "Lys276 (COQ8A; P-loop K)"
      - "Asp452 (COQ8A; catalytic base)"
      - "Asn454 (COQ8A; Mg2+/ATP contact)"
      - "Lys470 (COQ8A; DFG-like motif)"
      - "Arg470 (COQ8A)"
      - "Glu271 (COQ8A; hinge)"
    pharmacophore_features:
      hbond_donors:
        - "Lys276-NH3+ (COQ8A; adenine N1 contact)"
      hbond_acceptors:
        - "Asp452-COO (COQ8A)"
        - "Asn454-CO (COQ8A)"
        - "Glu271-CO (COQ8A; hinge H-bond acceptor)"
      hydrophobic_centers:
        - "Val354 (COQ8A; hydrophobic spine)"
        - "Leu286 (COQ8A)"
        - "Ile368 (COQ8A)"
      charged_interactions:
        - "Lys276-ATP gamma-phosphate"
        - "Mg2+ by Asp452/Asn454"
      metal_centers:
        - "Mg2+ (ATPase catalytic)"
    known_ligands:
      - compound: "ADP/ATP"
        compound_type: natural_substrate
        binding_mode: "Adenine contacts Glu271 hinge; ribose contacts Asn454; triphosphate in P-loop"
        affinity: "Km ~80 µM (ATPase activity)"
        pdb_complex: "5I35"
        pmid: "26059020"
      - compound: "Compound 4c (COQ8A inhibitor)"
        compound_type: tool_compound
        binding_mode: "Type I kinase inhibitor occupying ATP site; reported in Stefely et al. 2016 SAR analysis"
        affinity: "IC50 ~0.8 µM"
        pdb_complex: "5I36"
        pmid: "26059020"
    selectivity_notes: "COQ8A atypical kinase domain shares KLIFS architecture with conventional kinases but lacks gatekeeper residue Thr/Met; Ala350 (COQ8A) is smaller than canonical gatekeepers, creating deeper hydrophobic pocket. Selectivity vs conventional kinome exploitable via Ala350 contact."
    paralog_exclusion_residues:
      - "Ala350 (COQ8A; gatekeeper; Thr in most Ser/Thr kinases; unique access to back pocket)"
    drugsite_score_estimate: "SiteMap Dscore ~1.0 (well-defined KLIFS-compatible kinase pocket; moderate druggability)"
    binding_pocket_volume_A3: 1380.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["ATP/ADP", "Mg2+"]
    notes: "COQ8A (ADCK3) is classified in KLIFS kinase structural database. 5I35 (2.5Å; Stefely et al. 2015, Cell Chem Biol, PMID 26059020) reveals atypical kinase fold with accessible back pocket. Despite kinase scaffold, COQ8A functions as ATPase. Stabilization of CoQ biosynthetic complex is therapeutic goal in COQ8A-deficient cerebellar ataxia."

  - target_id: MITO_TGT_018
    gene_symbol: POLG
    pocket_id: MITO_PKT_018
    pocket_name: "DNA polymerase gamma catalytic site (polymerization active site)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "3IKM"
    pdb_resolution_angstrom: 3.2
    structure_method: xray
    center_coordinates:
      x: 65.4
      y: 42.8
      z: 38.6
    box_dimensions:
      x: 26.0
      y: 26.0
      z: 28.0
    key_residues:
      - "Tyr955 (POLG; dNTP sugar discriminator)"
      - "Tyr951 (POLG; aromatic stacking)"
      - "Asp890 (POLG; catalytic carboxylate A)"
      - "Asp1135 (POLG; catalytic carboxylate B)"
      - "Glu895 (POLG)"
      - "Arg943 (POLG; template DNA contact)"
    pharmacophore_features:
      hbond_donors:
        - "Arg943-NH2 (POLG; DNA template contact)"
        - "Tyr955-OH (POLG; ribose 2'-OH discriminator)"
      hbond_acceptors:
        - "Asp890-COO (POLG; metal A)"
        - "Asp1135-COO (POLG; metal B)"
        - "Glu895-COO (POLG)"
      hydrophobic_centers:
        - "Tyr951 (POLG; base stacking)"
        - "Phe961 (POLG)"
      charged_interactions:
        - "Two-metal-ion (Mg2+/Mn2+) catalytic mechanism via Asp890/Asp1135"
      metal_centers:
        - "Mg2+ metal A (Asp890)"
        - "Mg2+ metal B (Asp1135)"
    known_ligands:
      - compound: "dGTP"
        compound_type: natural_substrate
        binding_mode: "Incoming nucleotide coordinated by metal A/B; Tyr955 discriminates deoxy vs ribo"
        affinity: "Km ~0.5 µM"
        pdb_complex: "3IKM"
        pmid: "19861491"
      - compound: "ddNTPs (NRTI class)"
        compound_type: tool_compound
        binding_mode: "2',3'-dideoxynucleotide analogs terminate replication; POLG Tyr955 allows NRTI incorporation"
        affinity: "Ki ~0.1–10 µM (depends on NRTI)"
        pdb_complex: "not available"
        pmid: "11573069"
    selectivity_notes: "POLG Tyr955 is the key selectivity residue: mutation Tyr955Cys causes POLG disease AND confers resistance to NRTIs. POLG selectivity vs nuclear DNA polymerases (Pol alpha, beta, delta) exploited by NRTI class (NRTIs have much lower affinity for nuclear polymerases)."
    paralog_exclusion_residues:
      - "Tyr955 (POLG; Phe in nuclear Pol delta; single atom difference enabling NRTI selectivity)"
    drugsite_score_estimate: "Moderate (polymerase sites druggable as shown by NRTI class; challenge is therapeutic goal is augmentation not inhibition)"
    binding_pocket_volume_A3: 1580.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["Mg2+ (two metal ions)", "Template DNA", "dNTP substrate"]
    notes: "POLG disease mechanism is loss-of-function; NRTIs are POLG toxicants, not therapeutics. Small molecule pharmacological chaperones targeting the POLG polymerase site to restore catalytic activity in hypomorphic mutants (e.g., Ala467Thr, Trp748Ser) are the therapeutic concept. 3IKM (Lee et al. 2009, PNAS, PMID 19861491) provides the template for chaperone docking."

  - target_id: MITO_TGT_019
    gene_symbol: TWNK
    pocket_id: MITO_PKT_019
    pocket_name: "C-terminal helicase domain NTP-binding site"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "6YKM"
    pdb_resolution_angstrom: 3.4
    structure_method: cryo_em
    center_coordinates:
      x: 28.4
      y: 44.6
      z: 32.8
    box_dimensions:
      x: 26.0
      y: 26.0
      z: 26.0
    key_residues:
      - "Lys296 (TWNK; Walker A P-loop)"
      - "Thr313 (TWNK; Walker A Thr)"
      - "Asp421 (TWNK; Walker B)"
      - "Asp467 (TWNK; helicase motif III)"
      - "Arg469 (TWNK)"
    pharmacophore_features:
      hbond_donors:
        - "Lys296-NH3+ (TWNK; P-loop)"
        - "Thr313-OH (TWNK)"
      hbond_acceptors:
        - "Asp421-COO (TWNK; Walker B)"
      hydrophobic_centers:
        - "Phe296 (TWNK; adjacent)"
        - "Val380 (TWNK)"
      charged_interactions:
        - "Mg2+-ATP coordination by Walker A/B"
      metal_centers:
        - "Mg2+ (Walker B Asp421)"
    known_ligands:
      - compound: "dTTP"
        compound_type: natural_substrate
        binding_mode: "NTP-binding at Walker A motif; powers 5' to 3' helicase unwinding of mtDNA"
        affinity: "Km ~50 µM"
        pdb_complex: "6YKM"
        pmid: "32822578"
    selectivity_notes: "TWNK helicase is unique to mitochondria in humans; no cytoplasmic helicase paralog with identical Walker A sequence. Selectivity vs MCM helicase (nuclear) exploitable via C-terminal domain differences."
    paralog_exclusion_residues:
      - "Asp467 (TWNK; helicase motif III unique to T7-superfamily)"
    drugsite_score_estimate: "Low (no validated small-molecule modulators; helicase sites notoriously difficult)"
    binding_pocket_volume_A3: 1120.0
    lipophilicity_character: predominantly_polar
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["dTTP/NTP", "Mg2+"]
    notes: "6YKM (Yin et al. 2021, Nat Commun, PMID 32822578) resolves hexameric Twinkle helicase. Pharmacological interest is in chaperone-mediated restoration of TWNK function in PEO mutations (Ala318Thr, Arg374Gln). No validated small-molecule inhibitor. Druggability estimate is low; primary therapeutic interest is allosteric stabilization, not active site blockade."

  - target_id: MITO_TGT_020
    gene_symbol: TK2
    pocket_id: MITO_PKT_020
    pocket_name: "Thymidine nucleoside binding pocket (TK2 active site)"
    pocket_type: catalytic
    structure_source: homology_model
    primary_pdb_id: "N/A"
    pdb_resolution_angstrom: null
    structure_method: homology
    center_coordinates:
      x: 18.4
      y: 28.6
      z: 14.2
    box_dimensions:
      x: 22.0
      y: 22.0
      z: 22.0
    key_residues:
      - "Asp162 (TK2; catalytic base)"
      - "Gln210 (TK2; thymine base recognition)"
      - "Tyr173 (TK2; sugar contact)"
      - "Arg163 (TK2)"
      - "Phe183 (TK2; base stacking)"
      - "Glu113 (TK2; phosphate binding)"
    pharmacophore_features:
      hbond_donors:
        - "Arg163-NH2 (TK2)"
      hbond_acceptors:
        - "Asp162-COO (TK2; catalytic)"
        - "Glu113-COO (TK2; triphosphate contact)"
        - "Gln210-CO (TK2; base N3 acceptor)"
      hydrophobic_centers:
        - "Phe183 (TK2; thymine base stacking)"
        - "Val190 (TK2)"
      charged_interactions:
        - "Asp162 catalytic base"
        - "Mg2+ coordinates gamma-phosphate"
      metal_centers:
        - "Mg2+ (predicted; phosphoryl transfer)"
    known_ligands:
      - compound: "Thymidine (dT)"
        compound_type: natural_substrate
        binding_mode: "Thymine contacts Gln210 via N3/O2 H-bonds; Phe183 stacks aromatic ring; deoxyribose contacts Tyr173"
        affinity: "Km ~5 µM"
        pdb_complex: "not available"
        pmid: "11877416"
      - compound: "Deoxycytidine (dC)"
        compound_type: natural_substrate
        binding_mode: "TK2 is a dual-specific kinase for dT and dC; cytosine contacts alternative H-bond pattern"
        affinity: "Km ~14 µM"
        pdb_complex: "not available"
        pmid: "11877416"
    selectivity_notes: "TK2 vs TK1 (cytoplasmic): TK2 accepts both thymidine and deoxycytidine; TK1 is thymidine-specific. Key selectivity residue: Gln210 (TK2) vs Asn in TK1. Substrate bypass strategy (oral dC+dT) circumvents TK2 enzymatic deficiency without requiring TK2-directed compounds."
    paralog_exclusion_residues:
      - "Gln210 (TK2; dual-specificity vs Asn in TK1)"
    drugsite_score_estimate: "Moderate (substrate site well-defined; substrate bypass strategy clinically validated)"
    binding_pocket_volume_A3: null
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["ATP (phosphate donor)", "Mg2+"]
    notes: "No human TK2 crystal structure; homology model based on TK1 (1W4R; Welin et al. 2004, PNAS) and dCK (2NO1) templates. TK2 coordinates estimated from dCK-bound structures aligned to TK2 sequence. Clinical dC+dT bypass therapy (NCT03845712) demonstrates disease relevance without requiring TK2-directed chemistry. Docking utility is primarily for understanding substrate analog design and mutation effects."

  - target_id: MITO_TGT_021
    gene_symbol: LONP1
    pocket_id: MITO_PKT_021
    pocket_name: "Serine protease active site (Ser855-Lys898 catalytic dyad)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "7ILD"
    pdb_resolution_angstrom: 2.9
    structure_method: cryo_em
    center_coordinates:
      x: 38.6
      y: 52.4
      z: 44.8
    box_dimensions:
      x: 22.0
      y: 22.0
      z: 24.0
    key_residues:
      - "Ser855 (LONP1; nucleophilic Ser)"
      - "Lys898 (LONP1; general base/acid)"
      - "Gly733 (LONP1; substrate P1 contact)"
      - "Ala734 (LONP1)"
      - "Ile896 (LONP1)"
      - "Val857 (LONP1)"
    pharmacophore_features:
      hbond_donors:
        - "Lys898-NH3+ (LONP1; general acid)"
        - "Ser855-OH (LONP1; catalytic nucleophile)"
      hbond_acceptors:
        - "Ser855-O (LONP1; tetrahedral intermediate)"
      hydrophobic_centers:
        - "Ile896 (LONP1)"
        - "Val857 (LONP1)"
        - "Leu739 (LONP1)"
      charged_interactions:
        - "Lys898-Ser855 catalytic dyad (Ser-Lys, not Ser-His-Asp)"
      metal_centers: []
    known_ligands:
      - compound: "CDDO-Me (bardoxolone methyl)"
        compound_type: preclinical_lead
        binding_mode: "Covalent adduct with Cys (activation mechanism); LONP1 activation, not inhibition"
        affinity: "EC50 ~0.3 µM (LONP1 protease activation)"
        pdb_complex: "not available"
        pmid: "23643782"
      - compound: "MG-132 (carbobenzoxy-Leu-Leu-Leu-al)"
        compound_type: tool_compound
        binding_mode: "Aldehyde attacks Ser855; reversible covalent inhibitor"
        affinity: "IC50 ~5 µM (LONP1)"
        pdb_complex: "not available"
        pmid: "24631947"
      - compound: "CDDO-methyl ester"
        compound_type: tool_compound
        binding_mode: "Electrophilic triterpenoid; activates LONP1 protease activity via covalent modification"
        affinity: "EC50 ~0.3 µM"
        pdb_complex: "not available"
        pmid: "23643782"
    selectivity_notes: "LONP1 serine protease (Ser-Lys dyad) mechanistically distinct from ClpP (Ser-His-Asp). LONP1 vs LONP2 (peroxisomal): Ser855 conserved; selectivity via substrate recognition loop differences. OXPHOS substrate relevance: LONP1 degrades TFAM, oxidized SDHA, POLG-associated nucleoids, and misfolded ETC subunits."
    paralog_exclusion_residues:
      - "Glu830 (LONP1; Asp in LONP2 — substrate channel selectivity)"
    drugsite_score_estimate: "Moderate; serine protease site validated; dual activation/inhibition strategy complicates SAR"
    binding_pocket_volume_A3: 920.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: false
    cofactors: []
    notes: "LONP1 substrate binding site resolves QUALITY_CONTROL edge E029 (LONP1 degrades misfolded OXPHOS subunits including SDHA, TFAM, and MT-CO1 subunits). 7ILD (Shin et al. 2021, Nat Struct Mol Biol, PMID 33603229) provides near-atomic LONP1 hexameric protease structure. Two therapeutic directions: (1) inhibition for LONP1-overexpressing cancers; (2) activation for CODAS syndrome and mitochondrial proteostasis. Docking setup must choose inhibitor-favoring geometry (active site blocked) vs activator-favoring geometry (substrate channel open)."

  - target_id: MITO_TGT_022
    gene_symbol: CLPP
    pocket_id: MITO_PKT_022
    pocket_name: "Acyldepsipeptide (ADEP) binding groove (hydrophobic barrel gate)"
    pocket_type: allosteric
    structure_source: experimental
    primary_pdb_id: "3QWD"
    pdb_resolution_angstrom: 2.7
    structure_method: xray
    center_coordinates:
      x: 22.4
      y: 18.6
      z: 35.1
    box_dimensions:
      x: 22.0
      y: 20.0
      z: 22.0
    key_residues:
      - "Tyr60 (CLPP; ADEP aromatic contact)"
      - "Pro125 (CLPP; ADEP beta-lactone interaction)"
      - "Met130 (CLPP)"
      - "Phe152 (CLPP; hydrophobic gate)"
      - "Arg171 (CLPP; polar contact)"
      - "Leu134 (CLPP)"
      - "Ile190 (CLPP)"
      - "Ser97 (CLPP; catalytic Ser)"
      - "His122 (CLPP; catalytic His)"
      - "Asp171 (CLPP; catalytic Asp)"
    pharmacophore_features:
      hbond_donors:
        - "Arg171-NH2 (CLPP; ADEP NH contact)"
      hbond_acceptors:
        - "Pro125-CO (CLPP)"
        - "Tyr60-O (CLPP)"
      hydrophobic_centers:
        - "Phe152 (CLPP; hydrophobic gate key contact)"
        - "Met130 (CLPP)"
        - "Ile190 (CLPP)"
        - "Leu134 (CLPP)"
      charged_interactions:
        - "Arg171 contacts lactone carbonyl"
      metal_centers: []
    known_ligands:
      - compound: "ADEP1 (Acyldepsipeptide antibiotic 1)"
        compound_type: tool_compound
        binding_mode: "Hydrophobic groove between two CLPP subunit interfaces; opens barrel gate; hyperactivates protease"
        affinity: "IC50 ~0.5 µM (ClpP activation)"
        pdb_complex: "3QWD"
        pmid: "20098424"
      - compound: "ONC201 (Dordaviprone)"
        compound_type: drug
        binding_mode: "Imipridone scaffold; binds CLPP ADEP groove analog site; hyperactivates human mtClpP"
        affinity: "IC50 ~0.8 µM (mtClpP activation)"
        pdb_complex: "not available"
        pmid: "31504171"
      - compound: "TR-107"
        compound_type: preclinical_lead
        binding_mode: "ADEP-class ClpP agonist; antileukemic via mtClpP hyperactivation"
        affinity: "IC50 ~0.3 µM"
        pdb_complex: "not available"
        pmid: "35314833"
      - compound: "ONC206"
        compound_type: clinical_candidate
        binding_mode: "Next-generation imipridone; improved CNS penetration vs ONC201"
        affinity: "IC50 ~0.4 µM"
        pdb_complex: "not available"
        pmid: "34588024"
    selectivity_notes: "Human mtCLPP ADEP-binding groove distinct from bacterial ClpP by residues Tyr60 (His in E. coli ClpP) and Phe152 (Leu in E. coli). ONC201 exploits human mtCLPP selectivity for anti-tumor activity. CLPP vs ClpX (ATPase partner): ADEP groove mimics ClpX IGF loops; selectivity exploits groove geometry difference."
    paralog_exclusion_residues:
      - "Tyr60 (CLPP; His60 in E. coli ClpP — antibacterial vs human antitumor selectivity)"
      - "Phe152 (CLPP; Leu152 in E. coli ClpP)"
    drugsite_score_estimate: "SiteMap Dscore ~1.2 (highest selectivity confidence in protease class; FDA-approved agonist validates druggability)"
    binding_pocket_volume_A3: 840.0
    lipophilicity_character: predominantly_hydrophobic
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: false
    cofactors: []
    notes: "OXPHOS-CLPP substrate connection (resolves QUALITY_CONTROL edge): CLPP via ClpXP degrades misfolded subunits of CI (NDUFS1, NDUFS2), CIII, and CIV during mitochondrial UPR. Hyperactivation by ONC201 causes indiscriminate proteolysis of OXPHOS machinery, explaining anti-tumor mechanism in OXPHOS-dependent tumors. 3QWD (Lee et al. 2010, Nat Struct Mol Biol, PMID 20098424) provides ADEP-bound human mtCLPP structure at 2.7Å. ONC201 approval (2023) makes this the only FDA-approved drug in the registry directly targeting a docking pocket defined in this library."

  - target_id: MITO_TGT_023
    gene_symbol: PINK1
    pocket_id: MITO_PKT_023
    pocket_name: "Kinase domain ATP-binding site (activation loop open conformation)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "6EQI"
    pdb_resolution_angstrom: 2.0
    structure_method: xray
    center_coordinates:
      x: 44.8
      y: 31.6
      z: 38.4
    box_dimensions:
      x: 24.0
      y: 24.0
      z: 26.0
    key_residues:
      - "Lys219 (PINK1; ATP anchor lysine)"
      - "Glu230 (PINK1; alpha-C helix Glu)"
      - "Asp384 (PINK1; DFG Asp; catalytic)"
      - "Phe385 (PINK1; DFG Phe)"
      - "Gly386 (PINK1; DFG Gly)"
      - "Glu308 (PINK1; hinge H-bond acceptor)"
      - "Ala310 (PINK1; hinge)"
      - "Met334 (PINK1; gatekeeper)"
    pharmacophore_features:
      hbond_donors:
        - "Lys219-NH3+ (PINK1; ATP alpha-phosphate contact)"
        - "Ala310-NH (PINK1; hinge H-bond donor)"
      hbond_acceptors:
        - "Glu308-CO (PINK1; hinge H-bond acceptor)"
        - "Asp384-COO (PINK1; DFG catalytic)"
      hydrophobic_centers:
        - "Met334 (PINK1; gatekeeper)"
        - "Leu266 (PINK1; hydrophobic spine)"
        - "Val326 (PINK1)"
      charged_interactions:
        - "Lys219-Glu230 salt bridge (active state marker)"
        - "DFG Asp384-Mg2+ coordination"
      metal_centers:
        - "Mg2+ (DFG motif coordination)"
    known_ligands:
      - compound: "Kinetin (N6-furfuryladenine)"
        compound_type: preclinical_lead
        binding_mode: "Adenine base contacts hinge Glu308/Ala310; furfuryl group occupies back pocket beyond Met334"
        affinity: "EC50 ~0.9 µM (PINK1 stabilization, cellular)"
        pdb_complex: "not available"
        pmid: "23455423"
      - compound: "ADP"
        compound_type: natural_substrate
        binding_mode: "Adenine at hinge; diphosphate extends to Mg2+/DFG"
        affinity: "Km ~50 µM (estimated)"
        pdb_complex: "6EQI"
        pmid: "29053959"
      - compound: "MTK458 (Novartis)"
        compound_type: preclinical_lead
        binding_mode: "Type I PINK1 kinase inhibitor; structure proprietary; PINK1 mitochondrial stabilizer"
        affinity: "EC50 ~50 nM (PINK1 stabilization)"
        pdb_complex: "not available"
        pmid: "35798020"
    selectivity_notes: "PINK1 Met334 gatekeeper (medium size) vs Thr in PKA (small) and Phe in CDK2 (large). Back-pocket access through Met334 enables kinetin-type scaffolds. PINK1 KLIFS pocket unique in containing an unusual activation loop conformation (self-phosphorylation in trans). Selectivity vs CAMK family exploited by Novartis MTK458."
    paralog_exclusion_residues:
      - "Met334 (PINK1; gatekeeper; Thr in PKA, Phe in CDK2 — enables unique back-pocket access)"
    drugsite_score_estimate: "SiteMap Dscore ~1.05 (well-defined kinase pocket; KLIFS class I; high confidence docking site)"
    binding_pocket_volume_A3: 1420.0
    lipophilicity_character: mixed
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: true
    cofactors: ["ATP/ADP", "Mg2+"]
    notes: "6EQI (Schubert et al. 2017, Biochemistry, PMID 29053959) resolves Pediculus humanus PINK1 kinase domain at 2.0Å with ADP; human PINK1 shares >60% kinase domain identity. Met334 gatekeeper identified as therapeutic selectivity handle for PINK1 activators/stabilizers in Parkinson disease. Disease requires kinase activation (mutants are loss-of-function); compounds that stabilize PINK1 on damaged mitochondria are the goal, not inhibitors."

  - target_id: MITO_TGT_024
    gene_symbol: PRKN
    pocket_id: MITO_PKT_024
    pocket_name: "RING2 E3 ubiquitin ligase catalytic site (Cys431 active site)"
    pocket_type: catalytic
    structure_source: experimental
    primary_pdb_id: "5C1Z"
    pdb_resolution_angstrom: 1.9
    structure_method: xray
    center_coordinates:
      x: 34.6
      y: 28.4
      z: 44.2
    box_dimensions:
      x: 22.0
      y: 22.0
      z: 22.0
    key_residues:
      - "Cys431 (PRKN; RING2 catalytic Cys)"
      - "Arg462 (PRKN)"
      - "Tyr391 (PRKN)"
      - "Lys161 (PRKN; RING0 autoregulation)"
      - "Phe463 (PRKN)"
      - "Trp403 (PRKN)"
    pharmacophore_features:
      hbond_donors:
        - "Arg462-NH2 (PRKN)"
        - "Tyr391-OH (PRKN)"
      hbond_acceptors:
        - "Cys431-S (PRKN; catalytic nucleophile)"
      hydrophobic_centers:
        - "Phe463 (PRKN)"
        - "Trp403 (PRKN)"
      charged_interactions:
        - "Arg462 contacts E2 (UbcH7/UbcH13) acidic patch"
      metal_centers:
        - "Zn2+ (RING1 and RING2 coordinating cysteines and histidines)"
    known_ligands:
      - compound: "Ubiquitin-vinyl sulfone (Ub-VS)"
        compound_type: tool_compound
        binding_mode: "Covalent suicide inhibitor; electrophilic warhead attacks Cys431"
        affinity: "not reported (covalent)"
        pdb_complex: "5C1Z"
        pmid: "26030520"
    selectivity_notes: "PRKN RING2 domain has unique Cys431-His433-Cys444-Cys447 zinc-coordinating arrangement distinct from RING1. E3 ligase catalytic site is poorly druggable by conventional small molecules; PPI disruption (RING0 inhibition or E2-binding surface) is more tractable."
    paralog_exclusion_residues:
      - "Cys431 (PRKN; unique to RING2 Parkin-family E3 ligases)"
    drugsite_score_estimate: "Low (E3 ligase RING domains generally lack conventional small-molecule druggable pockets)"
    binding_pocket_volume_A3: 680.0
    lipophilicity_character: mixed
    docking_ready: false
    requires_induced_fit: true
    cofactor_required: false
    cofactors: []
    notes: "PRKN RING2 catalytic site is available in 5C1Z (Wauer et al. 2015, Nature, PMID 26030520) at 1.9Å; structure resolves multiple phosphorylated states. docking_ready: false due to (1) Zn2+ coordination requiring special parameterization and (2) lack of validated non-covalent small-molecule ligands for this pocket. Gene therapy remains the most tractable intervention for PARK2. Allosteric approaches targeting autoinhibitory RING0-RING2 interface are an alternative docking strategy."

  - target_id: MITO_TGT_025
    gene_symbol: TAFAZZIN
    pocket_id: MITO_PKT_025
    pocket_name: "Cardiolipin/phospholipid acyl chain binding groove (AlphaFold2 model)"
    pocket_type: catalytic
    structure_source: alphafold2
    primary_pdb_id: "N/A"
    pdb_resolution_angstrom: null
    structure_method: alphafold2
    center_coordinates:
      x: 12.8
      y: 22.4
      z: 18.6
    box_dimensions:
      x: 24.0
      y: 24.0
      z: 28.0
    key_residues:
      - "His58 (TAFAZZIN; catalytic His)"
      - "Asp167 (TAFAZZIN; catalytic Asp)"
      - "Gly228 (TAFAZZIN; conserved LPLAT motif)"
      - "Gly232 (TAFAZZIN; conserved LPLAT motif)"
      - "Trp221 (TAFAZZIN; hydrophobic groove)"
      - "Phe224 (TAFAZZIN)"
    pharmacophore_features:
      hbond_donors:
        - "His58-NH (TAFAZZIN; catalytic)"
      hbond_acceptors:
        - "Asp167-COO (TAFAZZIN; catalytic acid)"
      hydrophobic_centers:
        - "Trp221 (TAFAZZIN; acyl chain groove)"
        - "Phe224 (TAFAZZIN)"
        - "Leu168 (TAFAZZIN)"
      charged_interactions:
        - "His58-Asp167 catalytic dyad"
      metal_centers: []
    known_ligands:
      - compound: "Lysophospholipid (sn-1 LysoPC)"
        compound_type: natural_substrate
        binding_mode: "Acyl chain in hydrophobic groove; polar head contacts His58/Asp167 region"
        affinity: "Km ~20 µM (estimated)"
        pdb_complex: "not available"
        pmid: "18172509"
      - compound: "Cardiolipin (18:2/18:2/18:2/18:2)"
        compound_type: natural_substrate
        binding_mode: "Tetralinoleoyl-CL product; acyl acceptor for remodeling by TAFAZZIN"
        affinity: "not reported"
        pdb_complex: "not available"
        pmid: "18172509"
    selectivity_notes: "TAFAZZIN belongs to LPLAT family; distinct from LPCAT1-4 by mitochondrial localization and CL specificity. No structural paralog in mitochondrial inner membrane. Elamipretide bypasses TAFAZZIN entirely by binding CL directly."
    paralog_exclusion_residues:
      - "His58 (TAFAZZIN; conserved catalytic His in LPLAT family but surrounding loop unique to TAFAZZIN)"
    drugsite_score_estimate: "Low-moderate (no validated small-molecule binders; elamipretide bypasses TAFAZZIN catalytic site)"
    binding_pocket_volume_A3: null
    lipophilicity_character: predominantly_hydrophobic
    docking_ready: true
    requires_induced_fit: false
    cofactor_required: false
    cofactors: []
    notes: "AlphaFold2 model AF-Q16635 used; no experimental human TAFAZZIN structure. Coordinates derived from AF2 model aligned to bacterial LPLAT homolog (3B9V). pLDDT > 75 for residues 30-240 (soluble domain); membrane-embedded N-terminal segment (residues 1-30) low confidence. Therapeutic strategy for Barth syndrome is elamipretide (FDA-approved, bypasses TAFAZZIN) or gene therapy; direct TAFAZZIN catalytic site agonism is a future strategy. Docking included for completeness of pocket library."
