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Receptor Information

>1rk3 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 ID

VDX

InChI

InChI=1S/C27H44O3/c1-18(8-6-14-26(3,4)30)23-12-13-24-20(9-7-15-27(23,24)5)10-11-21-16-22(28)17-25(29)19(21)2/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b20-10+,21-11-/t18-,22-,23-,24+,25+,27-/m1/s1

InChIKey

GMRQFYUYWCNGIN-NKMMMXOESA-N

SMILES

Software	SMILES
CACTVS 3.341	C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)C[C@H](O)C3=C
OpenEye OEToolkits 1.5.0	CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C
CACTVS 3.341	C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C[CH](O)C3=C
OpenEye OEToolkits 1.5.0	C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C/3\C[C@H](C[C@@H](C3=C)O)O)C
ACDLabs 10.04	OC3C(=C)/C(=C\C=C1/CCCC2(C)C(C(C)CCCC(O)(C)C)CCC12)CC(O)C3

Formula

C27 H44 O3

Name

5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL;
1,25 DIHYDROXY VITAMIN D3

PDB chain

1rk3 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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Structure summary

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PDB	1rk3 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
Resolution	2.2 Å
Binding residue (original residue number in PDB)	Y143 V230 S233 I267 R270 S271 S274 W282 C284 H301 H393
Binding residue (residue number reindexed from 1)	Y21 V49 S52 I86 R89 S90 S93 W101 C103 H120 H212
Annotation score	4
Binding affinity	MOAD: Kd=0.37nM BindingDB: Ki=0.1nM,EC50=0.2nM

Enzyme Commision number

	Molecular Function
GO:0003677	DNA binding
GO:0004879	nuclear receptor activity

	Biological Process
GO:0006355	regulation of DNA-templated transcription

PDB	RCSB:1rk3, PDBe:1rk3, PDBj:1rk3
PDBsum	1rk3
PubMed	15065852
UniProt	P13053\|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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Structure of PDB 1rk3 Chain A Binding Site BS02