Structure of PDB 2o4j Chain A Binding Site BS02

Receptor Information
>2o4j 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]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMPLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMS
WDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMA
ICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQ
KLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNE
Ligand information
Ligand IDVD4
InChIInChI=1S/C27H42O3/c1-18(8-6-14-26(3,4)30)22-12-13-23-21(9-7-15-27(22,23)5)11-10-20-16-24(28)19(2)25(29)17-20/h10-11,23-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+,22-18-/t23-,24+,25+,27+/m0/s1
InChIKeyPCPYFQNISYYIPU-DUKKOGHCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C)CCCC(C)(C)O
CACTVS 3.341CC(/CCCC(C)(C)O)=C/1CC[C@H]2C(/CCC[C@]/12C)=C/C=C3\C[C@@H](O)C(=C)[C@H](O)C3
CACTVS 3.341CC(CCCC(C)(C)O)=C1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
OpenEye OEToolkits 1.5.0C/C(=C/1\CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C)/CCCC(C)(C)O
ACDLabs 10.04OC3\C(=C)C(O)CC(=C\C=C1/CCCC2(C(=C(\C)CCCC(O)(C)C)\CCC12)C)\C3
FormulaC27 H42 O3
Name(1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBL
DrugBank
ZINCZINC000016052266
PDB chain2o4j Chain A Residue 500 [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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PDB2o4j New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D(3) with conformationally restricted side chains: Evaluation of biological activity and structural determination of VDR-bound conformations.
Resolution1.74 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 R270 S271 S274 W282 C284 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 V49 S52 R89 S90 S93 W101 C103 H120 H212
Annotation score1
Binding affinityMOAD: Ki=0.08nM
PDBbind-CN: -logKd/Ki=10.10,Ki=0.08nM
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
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Biological Process
External links
PDB RCSB:2o4j, PDBe:2o4j, PDBj:2o4j
PDBsum2o4j
PubMed17227670
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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