Structure of PDB 5cw8 Chain A Binding Site BS01

Receptor Information
>5cw8 Chain A (length=176) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAQRERRKRILDATMAIASKGGYEAVQMRAVADRADVAVGTLYRYFPSKV
HLLVSALGREFSRIDAAGATPFQRLNFMVGKLNRAMQRNPLLTEAMTRAY
VFADASAASEVDQVEKLIDSMFARAMANGEPTEDQYHIARVISDVWLSNL
LAWLTRRASATDVSKRLDLAVRLLIG
Ligand information
Ligand ID55X
InChIInChI=1S/C48H75N7O15P2S/c1-27(32-12-13-33-31-11-10-29-22-30(56)14-17-47(29,5)34(31)15-18-48(32,33)6)8-7-9-28(2)45(61)73-21-20-50-36(57)16-19-51-43(60)40(59)46(3,4)24-68-72(65,66)67-23-35-39(70-71(62,63)64)38(58)44(69-35)55-26-54-37-41(49)52-25-53-42(37)55/h22,25-28,31-35,38-40,44,58-59H,7-21,23-24H2,1-6H3,(H,50,57)(H,51,60)(H,65,66)(H2,49,52,53)(H2,62,63,64)/t27-,28+,31+,32-,33+,34+,35?,38?,39?,40?,44?,47+,48-/m1/s1
InChIKeyVHFLMCCTKSGQAT-YKQRDCBHSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(SC(C(C)CCCC(C)C4CCC3C4(CCC2C1(CCC(=O)C=C1CCC23)C)C)=O)CNC(=O)CCNC(=O)C(O)C(COP(OCC5C(C(C(O5)n6cnc7c6ncnc7N)O)OP(O)(=O)O)(O)=O)(C)C
OpenEye OEToolkits 1.9.2C[C@H](CCC[C@H](C)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)[C@H]4CC[C@@H]5[C@@]4(CC[C@H]6[C@H]5CCC7=CC(=O)CC[C@]67C)C
CACTVS 3.385C[CH](CCC[CH](C)C(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)CO[P](O)(=O)OCC1OC(C(O)C1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH]4CC[CH]5[CH]6CCC7=CC(=O)CC[C]7(C)[CH]6CC[C]45C
CACTVS 3.385C[C@H](CCC[C@H](C)C(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)CO[P](O)(=O)OCC1OC(C(O)C1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@H]4CC[C@H]5[C@@H]6CCC7=CC(=O)CC[C@]7(C)[C@H]6CC[C@]45C
OpenEye OEToolkits 1.9.2CC(CCCC(C)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O)C4CCC5C4(CCC6C5CCC7=CC(=O)CCC67C)C
FormulaC48 H75 N7 O15 P2 S
NameS-{1-[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,7-dihydroxy-6,6-dimethyl-3-oxido-8,12 -dioxo-2,4-dioxa-9,13-diaza-3lambda~5~-phosphapentadecan-15-yl} (2S,6R)-6-[(8S,9S,10R,13R,14S,17R)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta [a]phenanthren-17-yl]-2-methylheptanethioate (non-preferred name);
S-{1-[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxi do-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (2S,6R)-6-[(8S,9S,10R,13R,14R,17S)-10,13-dimethyl-3-oxo-2,3,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta [a]phenanthren-17-yl]-2-methylheptanethioate (non-preferred name)
ChEMBL
DrugBank
ZINC
PDB chain5cw8 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5cw8 The Structure of the Transcriptional Repressor KstR in Complex with CoA Thioester Cholesterol Metabolites Sheds Light on the Regulation of Cholesterol Catabolism in Mycobacterium tuberculosis.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
E71 F72 N107 Y118 S161 W164 L168
Binding residue
(residue number reindexed from 1)
E60 F61 N89 Y100 S143 W146 L150
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,Kd=60nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000976 transcription cis-regulatory region binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

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Molecular Function

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Biological Process
External links
PDB RCSB:5cw8, PDBe:5cw8, PDBj:5cw8
PDBsum5cw8
PubMed26858250
UniProtP96856|KSTR_MYCTU HTH-type transcriptional repressor KstR (Gene Name=kstR)

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