Structure of PDB 1rjk Chain A Binding Site BS02

Receptor Information
>1rjk Chain A (length=239) 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
KLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand IDVDZ
InChIInChI=1S/C27H44O3/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/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+/t18-,22+,23-,24+,25+,27+/m0/s1
InChIKeyUHMPCVGLSKFXHR-NAQZCRMNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
ACDLabs 10.04OC3/C(=C)C(O)CC(=C\C=C1/CCCC2(C1CCC2C(C)CCCC(O)(C)C)C)\C3
CACTVS 3.385C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
CACTVS 3.385C[C@@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
OpenEye OEToolkits 1.7.5C[C@@H](CCCC(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
FormulaC27 H44 O3
Name5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIO L;
2-METHYLENE-19-NOR-(20S)-1ALPHA,25-DIHYDROXY-VITAMIN D3;
2MD
ChEMBLCHEMBL605525
DrugBank
ZINCZINC000004394162
PDB chain1rjk 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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PDB1rjk Molecular Structure of the Rat Vitamin D Receptor Ligand Binding Domain Complexed with 2-Carbon-Substituted Vitamin D(3) Hormone Analogues and a LXXLL-Containing Coactivator Peptide
Resolution1.99 Å
Binding residue
(original residue number in PDB)		Y143 S233 R270 S271 S274 W282 C284 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 S52 R89 S90 S93 W101 C103 H120 H212
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.00,Ki=0.1nM
BindingDB: Ki=0.1nM
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:1rjk, PDBe:1rjk, PDBj:1rjk
PDBsum1rjk
PubMed15065852
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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