Structure of PDB 3vrv Chain A Binding Site BS02

Receptor Information
>3vrv 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]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRPLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW
DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQK
LADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG
Ligand information
Ligand IDYSD
InChIInChI=1S/C28H46O3/c1-6-28(31,7-2)16-14-19(3)23-12-13-24-22(9-8-15-27(23,24)5)11-10-21-17-25(29)20(4)26(30)18-21/h10-11,19,23-26,29-31H,4,6-9,12-18H2,1-3,5H3/b22-11+/t19-,23-,24+,25-,26-,27-/m1/s1
InChIKeyCCJKDZZJQKPBID-IHLVXOQFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCC(CC)(CCC(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C)O
OpenEye OEToolkits 1.7.6CCC(CC)(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)O
ACDLabs 12.01OC3C(=C)\C(O)C/C(=C\C=C1/CCCC2(C)C(C(C)CCC(O)(CC)CC)CCC12)C3
CACTVS 3.370CCC(O)(CC)CC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
CACTVS 3.370CCC(O)(CC)CC[C@@H](C)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C3C[C@@H](O)C(=C)[C@H](O)C3
FormulaC28 H46 O3
Name(1R,3R,7E,17beta)-17-[(2R)-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBLCHEMBL2058272
DrugBank
ZINCZINC000084672155
PDB chain3vrv 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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PDB3vrv Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y143 L223 V230 S233 R270 S271 S274 W282 C284 V296 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 L41 V48 S51 R88 S89 S92 W100 C102 V114 H119 H211
Annotation score1
Binding affinityMOAD: ic50=0.029nM
PDBbind-CN: -logKd/Ki=10.54,IC50=0.029nM
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
View graph for
Biological Process
External links
PDB RCSB:3vrv, PDBe:3vrv, PDBj:3vrv
PDBsum3vrv
PubMed22512505
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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