Structure of PDB 6coj Chain A Binding Site BS01

Receptor Information
>6coj Chain A (length=295) Species: 101510 (Rhodococcus jostii RHA1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSKRDKRISLDDAVGELRSGMTIGIGGWGSRRKPMALVRALLRSDVTDLT
VVTYGGPDLGLLCSAGKVTKAYYGFVSLDSAPFYDPWFAKARTAGEIAVR
EMDAGMVKCGLEAAAARLPFLPIRAGLGSDVRRFWGDELRTVTSPYPDAS
GKSETLIAMPALNLDAALVHLNLGDKHGNAAYTGVDPYFDDLYCAAAEKR
FVSVERVVETEELVKTVPLQNLILNRMMVDGVVEAPNGAHFTLAGDSYGR
DEKFQRHYAESAKTPQAWQQFVATYLSGSEDDYQAAVKKFAEEQA
Ligand information
Ligand IDF8G
InChIInChI=1S/C32H48N7O20P3S/c1-16-4-5-17(40)21(32(16)8-6-20(42)57-32)30(46)63-11-10-34-19(41)7-9-35-28(45)25(44)31(2,3)13-55-62(52,53)59-61(50,51)54-12-18-24(58-60(47,48)49)23(43)29(56-18)39-15-38-22-26(33)36-14-37-27(22)39/h14-16,18,23-25,29,40,43-44H,4-13H2,1-3H3,(H,34,41)(H,35,45)(H,50,51)(H,52,53)(H2,33,36,37)(H2,47,48,49)/t16-,18-,23-,24-,25+,29-,32-/m1/s1
InChIKeyCOMHLEMSBYWTLA-LJKJHTHQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1CCC(=C(C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O[P](O)(O)=O)n3cnc4c(N)ncnc34)[C@@]15CCC(=O)O5)O
OpenEye OEToolkits 2.0.6CC1CCC(=C(C12CCC(=O)O2)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O)O)O
CACTVS 3.385C[CH]1CCC(=C(C(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O[P](O)(O)=O)n3cnc4c(N)ncnc34)[C]15CCC(=O)O5)O
OpenEye OEToolkits 2.0.6C[C@@H]1CCC(=C([C@@]12CCC(=O)O2)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)OP(=O)(O)O)O)O
ACDLabs 12.01c12n(cnc1c(N)ncn2)C3OC(C(C3O)OP(O)(=O)O)COP(OP(OCC(C(C(NCCC(NCCSC(C4=C(CCC(C45CCC(O5)=O)C)O)=O)=O)=O)O)(C)C)(O)=O)(=O)O
FormulaC32 H48 N7 O20 P3 S
NameS-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain6coj Chain B Residue 301 [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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PDB6coj IpdAB, a virulence factor inMycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase.
Resolution1.4 Å
Binding residue
(original residue number in PDB)
W29 Y85
Binding residue
(residue number reindexed from 1)
W28 Y84
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.40,Kd=0.4uM
Enzymatic activity
Enzyme Commision number 4.1.99.-
Gene Ontology
Molecular Function
GO:0008410 CoA-transferase activity
GO:0016829 lyase activity
Biological Process
GO:0006707 cholesterol catabolic process
GO:0008203 cholesterol metabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6coj, PDBe:6coj, PDBj:6coj
PDBsum6coj
PubMed29581275
UniProtQ0S7P9|IPDA_RHOJR Cholesterol ring-cleaving hydrolase IpdA subunit (Gene Name=ipdA)

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