Structure of PDB 6coj Chain B Binding Site BS01

Receptor Information
>6coj Chain B (length=248) Species: 101510 (Rhodococcus jostii RHA1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TEVTRAEYCAIACADIFSGAGEIMASPMATLPLIGARLARLTTEPDLLIT
DGEALIFADTPAVGAKAPIEGWMPFRKVFDVVASGRRHVVMGANQIDRHG
NQNLSAFGPLQQPTRQMFGVRGAPGNTINHPTSYWVGKHTSRVFCDTVDI
VSGVGYDQIDPENPAYRFHHLHRVVSNLGVFDFGGPDHTFRALSLHPGVT
ADQVADNTSFEVAGLADAGVTREPTDEELRLIREVLDPRSLRDREVSV
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)
M33 F84 R92 M96 G97 A98 N99 L109 F112 T119 R120 R126 N131 R147
Binding residue
(residue number reindexed from 1)
M28 F79 R87 M91 G92 A93 N94 L104 F107 T114 R115 R121 N126 R142
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.40,Kd=0.4uM
Enzymatic activity
Enzyme Commision number 4.1.99.-
Gene Ontology
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
UniProtQ0S7Q0|IPDB_RHOJR Cholesterol ring-cleaving hydrolase IpdB subunit (Gene Name=ipdB)

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