Structure of PDB 6co9 Chain B Binding Site BS01

Receptor Information
>6co9 Chain B (length=247) Species: 101510 (Rhodococcus jostii RHA1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVTRAEYCAIACADIFSGAGEIMASPMATLPLIGARLARLTTEPDLLITD
GEALIFADTPAVGAKAPIEGWMPFRKVFDVVASGRRHVVMGANQIDRHGN
QNLSAFGPLQQPTRQMFGVRGAPGNTINHPTSYWVGKHTSRVFCDTVDIV
SGVGYDQIDPENPAYRFHHLHRVVSNLGVFDFGGPDHTFRALSLHPGVTA
DQVADNTSFEVAGLADAGVTREPTDEELRLIREVLDPRSLRDREVSV
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 chain6co9 Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6co9 IpdAB, a virulence factor inMycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase.
Resolution1.602 Å
Binding residue
(original residue number in PDB)
M33 F84 R92 M96 G97 A98 N99 L109 F112 T119 R120 R126 N131
Binding residue
(residue number reindexed from 1)
M27 F78 R86 M90 G91 A92 N93 L103 F106 T113 R114 R120 N125
Annotation score3
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:6co9, PDBe:6co9, PDBj:6co9
PDBsum6co9
PubMed29581275
UniProtQ0S7Q0|IPDB_RHOJR Cholesterol ring-cleaving hydrolase IpdB subunit (Gene Name=ipdB)

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