Structure of PDB 5zwh Chain A Binding Site BS03

Receptor Information
>5zwh Chain A (length=237) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRLSMLPHLADLVSYS
IQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWD
CGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAIC
IVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKL
ADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand ID9N9
InChIInChI=1S/C27H36O3/c1-5-6-7-10-24(28)18(2)22-13-14-23-21(9-8-15-27(22,23)4)12-11-20-16-25(29)19(3)26(30)17-20/h5-6,11-12,18,22-23,25-26,29-30H,3,8-9,13-17H2,1-2,4H3/b6-5+,21-12+/t18-,22+,23-,25+,26+,27+/m0/s1
InChIKeyLQJPGHNFADIMOG-QHQWRQFTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC=CC#CC(=O)C(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
OpenEye OEToolkits 2.0.6C/C=C/C#CC(=O)[C@@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
ACDLabs 12.01C2(\C1CCC(C(C(=O)C#C[C@H]=CC)C)C1(CCC2)C)=C/C=C3\CC(/C(C(C3)O)=C)O
CACTVS 3.385C\C=C\C#CC(=O)[C@@H](C)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C3/C[C@@H](O)C(=C)[C@H](O)C3
CACTVS 3.385CC=CC#CC(=O)[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
FormulaC27 H36 O3
Name(E,2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-6-en-4-yn-3-one
ChEMBL
DrugBank
ZINC
PDB chain5zwh Chain A Residue 502 [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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PDB5zwh Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
Resolution2.38 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 R270 S271 S274 W282 H301
Binding residue
(residue number reindexed from 1)		Y21 V47 S50 R87 S88 S91 W99 H118
Annotation score1
Binding affinityMOAD: ic50=1.9nM
PDBbind-CN: -logKd/Ki=8.72,IC50=1.9nM
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
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Biological Process
External links
PDB RCSB:5zwh, PDBe:5zwh, PDBj:5zwh
PDBsum5zwh
PubMed29936834
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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