4YNK image
Deposition Date 2015-03-10
Release Date 2016-01-20
Last Version Date 2023-11-08
Entry Detail
PDB ID:
4YNK
Keywords:
Title:
Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound
Biological Source:
Source Organism:
Rattus norvegicus (Taxon ID: 10116)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.25
R-Value Work:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Vitamin D3 receptor,Vitamin D3 receptor
Gene (Uniprot):Vdr
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:Coactivator peptide drip from cDNA FLJ50196, highly similar to Peroxisome proliferator-activated receptor-binding protein
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
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
J.Med.Chem. 58 9510 9521 (2015)
PMID: 26613420 DOI: 10.1021/acs.jmedchem.5b00792

Abstact

Novel 19-norvitamin D analogues (ADYW1-4, 5a-d) in which an adamantyl diyne side chain is attached directly to the 17-position of the D ring are designed and stereoselectively synthesized. The adamantane ring of these analogues was expected to interfere with helix 12 (H12, activation function 2) of the vitamin D receptor (VDR) to modulate its activities. The analogue 5b binds to the VDR (7% of the natural hormone) and shows significant partial agonistic activity in transactivation assay. Compound 5b showed considerable selectivity in VDR target genes expressions in vitro, it was taken up by target cells 2-3 times more readily, and its lifetime was three times longer than the natural hormone. The X-ray crystal structure of 5b in complex with VDR reveals that the ligand binds similarly to the natural hormone, but the diyne moiety is slightly bent (angles around the diyne 5° to 8°) with respect to the original diyne vitamin D compound 6 in VDR (<1°) due to steric hindrance with helix 12.

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Primary Citation of related structures