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Receptor Information

>3vtd 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]

KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN

Ligand ID

TKD

InChI

InChI=1S/C36H52O3/c1-23(6-4-8-30(37)22-36-19-26-14-27(20-36)16-28(15-26)21-36)31-11-12-32-29(7-5-13-35(31,32)3)10-9-25-17-33(38)24(2)34(39)18-25/h9-10,23,26-28,30-34,37-39H,2,5-7,11-22H2,1,3H3/b29-10+/t23-,26-,27+,28-,30-,31-,32+,33-,34-,35-,36-/m1/s1

InChIKey

UFJLHOSCLNTAFF-OLECLGHFSA-N

SMILES

Software	SMILES
ACDLabs 12.01	OC6C(=C)\C(O)C/C(=C\C=C4/CCCC5(C)C(C(C)CC#CC(O)CC13CC2CC(C1)CC(C2)C3)CCC45)C6
CACTVS 3.370	C[C@H](CC#C[C@@H](O)CC12CC3CC(CC(C3)C1)C2)[C@H]4CC[C@H]5/C(CCC[C@]45C)=C/C=C6C[C@@H](O)C(=C)[C@H](O)C6
CACTVS 3.370	C[CH](CC#C[CH](O)CC12CC3CC(CC(C3)C1)C2)[CH]4CC[CH]5C(CCC[C]45C)=CC=C6C[CH](O)C(=C)[CH](O)C6
OpenEye OEToolkits 1.7.6	CC(CC#CC(CC12CC3CC(C1)CC(C3)C2)O)C4CCC5C4(CCCC5=CC=C6CC(C(=C)C(C6)O)O)C
OpenEye OEToolkits 1.7.6	C[C@H](CC#C[C@H](CC12CC3CC(C1)CC(C3)C2)O)[C@H]4CC[C@@H]\5[C@@]4(CCC/C5=C\C=C6C[C@H](C(=C)[C@@H](C6)O)O)C

Formula

C36 H52 O3

Name

(1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol

ChEMBL

DrugBank

ZINC

PDB chain

3vtd 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	3vtd Combination of Triple Bond and Adamantane Ring on the Vitamin D Side Chain Produced Partial Agonists for Vitamin D Receptor.
Resolution	2.7 Å
Binding residue (original residue number in PDB)	Y143 L223 A227 V230 S233 M268 R270 S271 S274 W282 V296 H301 H393
Binding residue (residue number reindexed from 1)	Y21 L43 A47 V50 S53 M88 R90 S91 S94 W102 V116 H121 H213
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=7.92,IC50=12nM

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:3vtd, PDBe:3vtd, PDBj:3vtd
PDBsum	3vtd
PubMed	24773565
UniProt	P13053\|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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Structure of PDB 3vtd Chain A Binding Site BS02