Structure of PDB 3vrt Chain A Binding Site BS02

Receptor Information
>3vrt Chain A (length=238) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMS
WDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMA
ICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQ
KLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG
Ligand information
Ligand IDYS2
InChIInChI=1S/C24H38O3/c1-16(6-5-13-25)20-10-11-21-19(7-4-12-24(20,21)3)9-8-18-14-22(26)17(2)23(27)15-18/h8-9,16,20-23,25-27H,2,4-7,10-15H2,1,3H3/b19-9+/t16-,20-,21+,22-,23-,24-/m1/s1
InChIKeyJPGZPBYJMAWTHF-HCMYXCKPSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C[C@H](CCCO)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
OpenEye OEToolkits 1.7.6CC(CCCO)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
OpenEye OEToolkits 1.7.6C[C@H](CCCO)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
CACTVS 3.370C[CH](CCCO)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
ACDLabs 12.01OC3C(=C)\C(O)C/C(=C\C=C1/CCCC2(C)C(C(C)CCCO)CCC12)C3
FormulaC24 H38 O3
Name(1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBLCHEMBL1212956
DrugBank
ZINCZINC000058538292
PDB chain3vrt 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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PDB3vrt Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y143 S233 I264 R270 S271 S274 W282 C284 V296 H393
Binding residue
(residue number reindexed from 1)		Y20 S52 I83 R89 S90 S93 W101 C103 V115 H212
Annotation score1
Binding affinityMOAD: ic50=2.7nM
PDBbind-CN: -logKd/Ki=8.57,IC50=2.7nM
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:3vrt, PDBe:3vrt, PDBj:3vrt
PDBsum3vrt
PubMed22512505
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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