Structure of PDB 3w5t Chain A Binding Site BS02

Receptor Information
>3w5t Chain A (length=242) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEI
Ligand information
Ligand IDLHP
InChIInChI=1S/C27H44O4/c1-5-25(30)31-19-12-14-26(3)18(16-19)7-8-20-22-10-9-21(17(2)6-11-24(28)29)27(22,4)15-13-23(20)26/h17-23H,5-16H2,1-4H3,(H,28,29)/t17-,18-,19-,20+,21-,22+,23+,26+,27-/m1/s1
InChIKeyRDIKLWFVJHJCMN-RMXYKXGFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCC(=O)OC1CCC2(C(C1)CCC3C2CCC4(C3CCC4C(C)CCC(=O)O)C)C
OpenEye OEToolkits 1.7.6CCC(=O)O[C@@H]1CC[C@]2([C@@H](C1)CC[C@@H]3[C@@H]2CC[C@]4([C@H]3CC[C@@H]4[C@H](C)CCC(=O)O)C)C
ACDLabs 12.01O=C(O)CCC(C4C3(C(C2C(C1(CCC(OC(=O)CC)CC1CC2)C)CC3)CC4)C)C
CACTVS 3.370CCC(=O)O[C@@H]1CC[C@@]2(C)[C@H](CC[C@H]3[C@@H]4CC[C@H]([C@H](C)CCC(O)=O)[C@@]4(C)CC[C@H]23)C1
CACTVS 3.370CCC(=O)O[CH]1CC[C]2(C)[CH](CC[CH]3[CH]4CC[CH]([CH](C)CCC(O)=O)[C]4(C)CC[CH]23)C1
FormulaC27 H44 O4
Name(3beta,5beta,9beta)-3-(propanoyloxy)cholan-24-oic acid;
Lithocholic acid propionate
ChEMBL
DrugBank
ZINCZINC000095921179
PDB chain3w5t Chain A Residue 500 [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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PDB3w5t Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
Resolution2.29 Å
Binding residue
(original residue number in PDB)		Y143 A227 I267 S271 S274 W282 V296 H301 H393 V414
Binding residue
(residue number reindexed from 1)		Y21 A47 I87 S91 S94 W102 V116 H121 H213 V234
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.52,IC50=30uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3w5t, PDBe:3w5t, PDBj:3w5t
PDBsum3w5t
PubMed23723390
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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