Structure of PDB 8ovd Chain G Binding Site BS05

Receptor Information
>8ovd Chain G (length=380) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPTDAELAEMSREELVKLGGKIDGVETIFKEPRWPVPGTKAEKRTERLVA
YWLMLGGLSGLALLLVFLFWPWEYQPFGSEGEFLYSLATPLYGLTFGLSI
LSIGIGAVLFQKKFIPEEISVQDRHDGRSPEVHRKTVAANLTDALEGSTL
KRRKVIGLSLGIGLGAFGAGTLVAFIGGLIKNPWKPVVPTAEGKKAVLWT
SGWTPRFKGETIYLARATGRPGESPFVKMRPEDIDAGGMETVFPWRESDG
DGTTVESEHKLTEIAMGVRNPVMLIRIKPADMHRVIKRKGQESFNFGELF
AYTKVCSHLGCPSSLYEQQTYRILCPCHQSQFDALEFAKPIFGPAARALA
QLPITIDEDGYLVANGDFVEPVGPAFWERK
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 G Residue 903 [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)
K235 W239 D407 V409 E418 K420
Binding residue
(residue number reindexed from 1)
K195 W199 D367 V369 E378 K380
Annotation score1
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051537 2 iron, 2 sulfur cluster binding
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:8ovd, PDBe:8ovd, PDBj:8ovd
PDBsum8ovd
PubMed38902248
UniProtA0R051

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