Structure of PDB 5zwi Chain A Binding Site BS02

Receptor Information
>5zwi Chain A (length=240) 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
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand ID9KX
InChIInChI=1S/C27H38O3/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/h5-7,10-12,18,22-23,25-26,29-30H,3,8-9,13-17H2,1-2,4H3/b6-5+,10-7+,21-12+/t18-,22+,23-,25+,26+,27+/m0/s1
InChIKeyNXEUFUPQFMVYDT-SVJWBRFGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC=CC=CC(=O)[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
CACTVS 3.385C/C=C/C=C/C(=O)[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
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=C/C(=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 12.01OC\1CC(/CC(C/1=C)O)=C/C=C3/C2C(C(CC2)C(C)C(=O)\C=C\[C@H]=CC)(CCC3)C
FormulaC27 H38 O3
Name(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-4,6-diene-3-one
ChEMBLCHEMBL4161578
DrugBank
ZINC
PDB chain5zwi 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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PDB5zwi Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y143 L223 A227 V230 S233 R270 S271 S274 W282 V296
Binding residue
(residue number reindexed from 1)		Y21 L43 A47 V50 S53 R90 S91 S94 W102 V116
Annotation score1
Binding affinityMOAD: ic50=2.3nM
PDBbind-CN: -logKd/Ki=8.64,IC50=2.3nM
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:5zwi, PDBe:5zwi, PDBj:5zwi
PDBsum5zwi
PubMed29936834
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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