Structure of PDB 5zwf Chain A Binding Site BS02

Receptor Information
>5zwf 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 ID9KR
InChIInChI=1S/C27H40O3/c1-5-7-22(28)12-9-18(2)23-13-14-24-21(8-6-15-27(23,24)4)11-10-20-16-25(29)19(3)26(30)17-20/h5,7,10-11,18,23-26,29-30H,3,6,8-9,12-17H2,1-2,4H3/b7-5+,21-11+/t18-,23-,24+,25-,26-,27-/m1/s1
InChIKeyVGMKRRGYTONKLW-FOWSJJJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C/C=C/C(=O)CC[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
CACTVS 3.385C/C=C/C(=O)CC[C@@H](C)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C\3C[C@@H](O)C(=C)[C@H](O)C\3
ACDLabs 12.01O=C(\C=C\C)CCC(C)C1CCC2C1(CCCC2=[C@H][C@H]=C3CC(C(\C(C3)O)=C)O)C
CACTVS 3.385CC=CC(=O)CC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
OpenEye OEToolkits 2.0.6CC=CC(=O)CCC(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
FormulaC27 H40 O3
Name(E,7R)-7-[(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-2-en-4-one
ChEMBLCHEMBL4176693
DrugBank
ZINC
PDB chain5zwf Chain A Residue 501 [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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PDB5zwf Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y143 S233 R270 S271 S274 W282 V296 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 S50 R87 S88 S91 W99 V113 H118 H210
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.74,IC50=1.8nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5zwf, PDBe:5zwf, PDBj:5zwf
PDBsum5zwf
PubMed29936834
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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