Structure of PDB 8ovd Chain N Binding Site BS03

Receptor Information
>8ovd Chain N (length=533) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DFAKLAAAQGDAIDSRYHPSAAVRRQLNKVFPTHWSFLLGEIALYSFIIL
LLTGVWLTLFFDPSMAHVTYDGVYQPLRGVQMSRAYETALDISFEVRGGL
FVRQVHHWAALMFAASIMVHLARIFFTGAFRRPREANWVIGSLLLILAMF
EGFFGYSLPDDLLSGTGIRAALSGITMGIPVIGTWMHWALFGGDFPGEIL
IPRLYALHILLIPGIILALIGAHLALVWFQKHTQFPGPGRTETNVVGVRV
MPVFAVKSGAFFAMITGVLGLMGGLLTINPIWNLGPYKPSQVSAGSQPDF
YMMWTDGLIRLWPAWEFYPFGHTIPQGVWVAVGMGLVFALLIAYPFIEKK
VTGDDAHHNLLQRPRDVPVRTAIGSMAIALYLLLTFACMNDIIALKFHIS
LNATTWIGRIGMVVLPAIVYFVAYRWAISLQRSDREVLEHGVETGIIKRL
PHGAYVELHQPLGPVDEHGHPIPLEYAGAPLPKRMNKLGSGGAPGTGSFL
FPDPAVEHEALTEAAHASEHKSLTALKEHQDRI
Ligand information
Ligand IDIZL
InChIInChI=1S/C74H133O39P/c1-5-8-10-12-14-16-21-26-30-47(78)100-36-43-51(82)56(87)64(95)72(108-43)110-66-60(91)58(89)61(92)67(69(66)113-114(97,98)103-35-40(104-48(79)31-27-23-17-15-13-11-9-6-2)34-99-46(77)29-25-22-19-18-20-24-28-39(4)7-3)111-73-65(96)57(88)53(84)45(109-73)37-101-70-62(93)55(86)52(83)44(107-70)38-102-74-68(59(90)50(81)42(33-76)106-74)112-71-63(94)54(85)49(80)41(32-75)105-71/h39-45,49-76,80-96H,5-38H2,1-4H3,(H,97,98)/t39-,40-,41-,42-,43-,44-,45-,49-,50-,51-,52-,53-,54+,55+,56+,57+,58-,59+,60-,61+,62+,63+,64+,65+,66-,67-,68+,69-,70+,71-,72-,73-,74+/m1/s1
InChIKeyRFJQNGLGKTXNKA-YXJCWACHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCCCCCCCC(=O)OC[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H]([C@@H]2OP(=O)(O)OC[C@@H](COC(=O)CCCCCCCC[C@H](C)CC)OC(=O)CCCCCCCCCC)O[C@@H]3[C@H]([C@H]([C@@H]([C@H](O3)CO[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO[C@@H]5[C@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O[C@@H]6[C@H]([C@H]([C@@H]([C@H](O6)CO)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O
CACTVS 3.385CCCCCCCCCCC(=O)OC[C@H]1O[C@H](O[C@@H]2[C@H](O)[C@@H](O)[C@H](O)[C@@H](O[C@H]3O[C@H](CO[C@H]4O[C@H](CO[C@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]5O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]6O)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H]2O[P](O)(=O)OC[C@@H](COC(=O)CCCCCCCC[C@H](C)CC)OC(=O)CCCCCCCCCC)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.7CCCCCCCCCCC(=O)OCC1C(C(C(C(O1)OC2C(C(C(C(C2OP(=O)(O)OCC(COC(=O)CCCCCCCCC(C)CC)OC(=O)CCCCCCCCCC)OC3C(C(C(C(O3)COC4C(C(C(C(O4)COC5C(C(C(C(O5)CO)O)O)OC6C(C(C(C(O6)CO)O)O)O)O)O)O)O)O)O)O)O)O)O)O)O
CACTVS 3.385CCCCCCCCCCC(=O)OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](O)[CH](O[CH]3O[CH](CO[CH]4O[CH](CO[CH]5O[CH](CO)[CH](O)[CH](O)[CH]5O[CH]6O[CH](CO)[CH](O)[CH](O)[CH]6O)[CH](O)[CH](O)[CH]4O)[CH](O)[CH](O)[CH]3O)[CH]2O[P](O)(=O)OC[CH](COC(=O)CCCCCCCC[CH](C)CC)OC(=O)CCCCCCCCCC)[CH](O)[CH](O)[CH]1O
FormulaC74 H133 O39 P
Name[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate
ChEMBL
DrugBank
ZINC
PDB chain8ovd Chain M Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ovd Long-range charge transfer mechanism of the III 2 IV 2 mycobacterial supercomplex.
Resolution2.3 Å
Binding residue
(original residue number in PDB)
V184 W188 H325
Binding residue
(residue number reindexed from 1)
V181 W185 H322
Annotation score1
Gene Ontology
Molecular Function
GO:0008121 ubiquinol-cytochrome-c reductase activity
Biological Process
GO:1902600 proton transmembrane transport
Cellular Component
GO:0016020 membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8ovd, PDBe:8ovd, PDBj:8ovd
PDBsum8ovd
PubMed38902248
UniProtA0R052

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