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Structure of PDB 4w97 Chain A Binding Site BS01

Receptor Information
>4w97 Chain A (length=196) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVAGQVNSRRGELLELAAAMFAERGLRATTVRDIADGAGILSGSLYHHFA
SKEEMVDELLRGFLDWLFARYRDIVDSTANPLERLQGLFMASFEAIEHHH
AQVVIYQDEAQRLASQPRFSYIEDRNKQQRKMWVDVLNQGIEEGYFRPDL
DVDLVYRFIRDTTWVSVRWYRPGGPLTAQQVGQQYLAIVLGGITKE
Ligand information
Ligand IDUCA
InChIInChI=1S/C34H52N7O19P3S/c1-33(2,28(47)31(48)37-11-9-23(44)36-12-13-64-24(45)7-4-18-19-5-6-22(43)34(19,3)10-8-20(18)42)15-57-63(54,55)60-62(52,53)56-14-21-27(59-61(49,50)51)26(46)32(58-21)41-17-40-25-29(35)38-16-39-30(25)41/h16-19,21,26-28,32,46-47H,4-15H2,1-3H3,(H,36,44)(H,37,48)(H,52,53)(H,54,55)(H2,35,38,39)(H2,49,50,51)/t18-,19-,21+,26+,27+,28-,32+,34-/m0/s1
InChIKeyIWNWMTZIJPUDPV-MDQHZGBLSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1CCC2C1(C)CCC(=O)C2CCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c(ncnc34)N)C(O)C5OP(=O)(O)O
CACTVS 3.385CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CC[CH]4[CH]5CCC(=O)[C]5(C)CCC4=O
CACTVS 3.385CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CC[C@H]4[C@@H]5CCC(=O)[C@@]5(C)CCC4=O
OpenEye OEToolkits 1.7.6CC12CCC(=O)C(C1CCC2=O)CCC(=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
OpenEye OEToolkits 1.7.6C[C@]12CCC(=O)[C@H]([C@@H]1CCC2=O)CCC(=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
FormulaC34 H52 N7 O19 P3 S
NameS-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-[(3aS,4S,7aS)-7a-methyl-1,5-bis(oxidanylidene)-2,3,3a,4,6,7-hexahydroinden-4-yl]propanethioate;
HIP-CoA
ChEMBL
DrugBank
ZINCZINC000219083543
PDB chain4w97 Chain A 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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PDB4w97 Structural and Functional Characterization of a Ketosteroid Transcriptional Regulator of Mycobacterium tuberculosis.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y108 Q109 N128 Q131 R159 R162 D163 W166
Binding residue
(residue number reindexed from 1)		Y106 Q107 N126 Q129 R157 R160 D161 W164
Annotation score1
Binding affinityMOAD: Kd=0.08uM
PDBbind-CN: -logKd/Ki=7.10,Kd=0.08uM
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
Biological Process
GO:0006355 regulation of DNA-templated transcription

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4w97, PDBe:4w97, PDBj:4w97
PDBsum4w97
PubMed25406313
UniProtP9WMB9|KSTR2_MYCTU HTH-type transcriptional repressor KstR2 (Gene Name=kstR2)

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