Structure of PDB 1rkh Chain A Binding Site BS02

Receptor Information
>1rkh Chain A (length=242) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEI
Ligand information
Ligand IDVD2
InChIInChI=1S/C27H46O3/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/h10-11,18-19,22-25,28-30H,6-9,12-17H2,1-5H3/b20-10-,21-11+/t18-,19+,22-,23+,24-,25-,27-/m1/s1
InChIKeyOZPNRDQPQFOURL-VJPYOZRWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(CC(=CC=C2CCCC3(C2CCC3C(C)CCCC(C)(C)O)C)CC1O)O
CACTVS 3.341C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2\C(CCC[C@]12C)=C\C=C/3C[C@@H](O)[C@H](C)[C@H](O)C/3
CACTVS 3.341C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)[CH](C)[CH](O)C3
OpenEye OEToolkits 1.5.0CC1[C@@H](CC(=C\C=C\2/CCC[C@]3([C@H]2CC[C@@H]3[C@H](C)CCCC(C)(C)O)C)C[C@H]1O)O
ACDLabs 10.04OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)\CC(O)C3C
FormulaC27 H46 O3
Name5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL-CYCLOHEXANE-1,3-DIOL;
2-ALPHA-METHYL-19-NOR-1,25-DIHYDROXYVITAMIN D3;
2AM20R
ChEMBLCHEMBL3084958
DrugBank
ZINC
PDB chain1rkh Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rkh 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
Resolution2.28 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 M268 R270 S271 S274 W282 C284 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 V50 S53 M88 R90 S91 S94 W102 C104 H121 H213
Annotation score1
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:1rkh, PDBe:1rkh, PDBj:1rkh
PDBsum1rkh
PubMed15065852
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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