Structure of PDB 5zwe Chain A Binding Site BS02

Receptor Information
>5zwe 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 ID9K0
InChIInChI=1S/C26H38O3/c1-5-21(27)11-8-17(2)22-12-13-23-20(7-6-14-26(22,23)4)10-9-19-15-24(28)18(3)25(29)16-19/h5,9-10,17,22-25,28-29H,1,3,6-8,11-16H2,2,4H3/b20-10+/t17-,22-,23+,24-,25-,26-/m1/s1
InChIKeyXVGVVMUDYCUDFM-VMKNJNNYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](CCC(=O)C=C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
CACTVS 3.385C[C@H](CCC(=O)C=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(CCC(=O)C=C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
ACDLabs 12.01O=C(\C=C)CCC(C)C1CCC2C1(CCCC2=[C@H][C@H]=C3CC(C(\C(C3)O)=C)O)C
OpenEye OEToolkits 2.0.6C[C@H](CCC(=O)C=C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
FormulaC26 H38 O3
Name(6R)-6-[(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]hept-1-en-3-one
ChEMBLCHEMBL4176277
DrugBank
ZINC
PDB chain5zwe 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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PDB5zwe Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
Resolution2.72 Å
Binding residue
(original residue number in PDB)		L226 V230 S233 R270 S271 S274 W282 H301 L309
Binding residue
(residue number reindexed from 1)		L46 V50 S53 R90 S91 S94 W102 H121 L129
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.96,IC50=1.1nM
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
View graph for
Biological Process
External links
PDB RCSB:5zwe, PDBe:5zwe, PDBj:5zwe
PDBsum5zwe
PubMed29936834
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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