Structure of PDB 3vrw Chain A Binding Site BS02

Receptor Information
>3vrw 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]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMPLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMS
WDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMA
ICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQ
KLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG
Ligand information
Ligand IDYS5
InChIInChI=1S/C32H54O3/c1-7-10-12-26(21-32(35,8-2)9-3)22(4)27-16-17-28-25(13-11-18-31(27,28)6)15-14-24-19-29(33)23(5)30(34)20-24/h14-15,22,26-30,33-35H,5,7-13,16-21H2,1-4,6H3/b25-15+/t22-,26+,27-,28+,29-,30-,31-/m1/s1
InChIKeyOILLQCLQUXHGBN-PWPPSVFISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCC(CC(CC)(CC)O)C(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
OpenEye OEToolkits 1.7.6CCCC[C@@H](CC(CC)(CC)O)[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CCCC2=CC=C3C[C@H](C(=C)[C@@H](C3)O)O)C
CACTVS 3.370CCCC[C@@H](CC(O)(CC)CC)[C@@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
ACDLabs 12.01OC3C(=C)\C(O)C/C(=C\C=C1/CCCC2(C)C(C(C)C(CCCC)CC(O)(CC)CC)CCC12)C3
CACTVS 3.370CCCC[CH](CC(O)(CC)CC)[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
FormulaC32 H54 O3
Name(1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBLCHEMBL2058274
DrugBank
ZINCZINC000084725316
PDB chain3vrw Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vrw 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 R270 S271 S274 W282 C284 V296 H301 L305 H393
Binding residue
(residue number reindexed from 1)		Y21 S52 R89 S90 S93 W101 C103 V115 H120 L124 H212
Annotation score1
Binding affinityMOAD: ic50=0.41nM
PDBbind-CN: -logKd/Ki=9.39,IC50=0.41nM
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:3vrw, PDBe:3vrw, PDBj:3vrw
PDBsum3vrw
PubMed22512505
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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