Structure of PDB 3vru Chain A Binding Site BS02

Receptor Information
>3vru 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]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW
DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQK
LADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand IDYS3
InChIInChI=1S/C26H42O3/c1-17(12-14-25(3,4)29)21-10-11-22-20(7-6-13-26(21,22)5)9-8-19-15-23(27)18(2)24(28)16-19/h8-9,17,21-24,27-29H,2,6-7,10-16H2,1,3-5H3/b20-9+/t17-,21-,22+,23-,24-,26-/m1/s1
InChIKeyJLJBOAPFTSKXIR-PXIOBPQKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C[CH](CCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
OpenEye OEToolkits 1.7.6C[C@H](CCC(C)(C)O)[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[C@H](CCC(C)(C)O)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C3C[C@@H](O)C(=C)[C@H](O)C3
OpenEye OEToolkits 1.7.6CC(CCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
ACDLabs 12.01OC3C(=C)\C(O)C\C(=C\C=C1/CCCC2(C)C(C(C)CCC(O)(C)C)CCC12)C3
FormulaC26 H42 O3
Name(1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBLCHEMBL1214510
DrugBank
ZINCZINC000058583723
PDB chain3vru 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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PDB3vru Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 R270 S271 S274 W282 C284 V296 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 V48 S51 R88 S89 S92 W100 C102 V114 H119 H211
Annotation score1
Binding affinityMOAD: ic50=0.1nM
PDBbind-CN: -logKd/Ki=10.00,IC50=0.10nM
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:3vru, PDBe:3vru, PDBj:3vru
PDBsum3vru
PubMed22512505
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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