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Receptor Information

>4ynk 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 ID

YW2

InChI

InChI=1S/C34H44O3/c1-22-30(35)17-23(18-31(22)36)9-10-27-6-5-13-33(2)28(11-12-29(27)33)7-3-4-8-32(37)34-19-24-14-25(20-34)16-26(15-24)21-34/h9-10,24-26,28-32,35-37H,1,5-6,11-21H2,2H3/b27-10+/t24-,25+,26-,28-,29-,30+,31+,32+,33+,34-/m0/s1

InChIKey

BFGRTJZGAMDLML-XMEPBAHGSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.9.2	CC12CCCC(=CC=C3CC(C(=C)C(C3)O)O)C1CCC2C#CC#CC(C45CC6CC(C4)CC(C6)C5)O
OpenEye OEToolkits 1.9.2	C[C@]12CCC/C(=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)/[C@@H]1CC[C@@H]2C#CC#C[C@H](C45CC6CC(C4)CC(C6)C5)O
CACTVS 3.385	C[C]12CCCC(=CC=C3C[CH](O)C(=C)[CH](O)C3)[CH]1CC[CH]2C#CC#C[CH](O)C45CC6CC(CC(C6)C4)C5
CACTVS 3.385	C[C@]12CCCC(=C/C=C/3C[C@@H](O)C(=C)[C@H](O)C/3)\[C@@H]1CC[C@@H]2C#CC#C[C@@H](O)C45CC6CC(CC(C6)C4)C5
ACDLabs 12.01	C5(C#CC#CC(O)C13CC2CC(C1)CC(C2)C3)C4(CCCC(C4CC5)=[C@H][C@H]=C6CC(O)/C(C(C6)O)=C)C

Formula

C34 H44 O3

Name

(1R,3R,7E,17beta)-17-{(5S)-5-hydroxy-5-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-1-yl]penta-1,3-diyn-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol

ChEMBL

DrugBank

ZINC

PDB chain

4ynk 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	4ynk Synthesis, Biological Activities, and X-ray Crystal Structural Analysis of 25-Hydroxy-25(or 26)-adamantyl-17-[20(22),23-diynyl]-21-norvitamin D Compounds
Resolution	2.3 Å
Binding residue (original residue number in PDB)	Y143 A227 V230 S233 R270 S271 S274 W282 Y291 H301 L309 H393 L410
Binding residue (residue number reindexed from 1)	Y21 A46 V49 S52 R89 S90 S93 W101 Y110 H120 L128 H212 L229
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=8.30,IC50=5nM

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:4ynk, PDBe:4ynk, PDBj:4ynk
PDBsum	4ynk
PubMed	26613420
UniProt	P13053\|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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Structure of PDB 4ynk Chain A Binding Site BS02