5XPL image
Entry Detail
PDB ID:
5XPL
Keywords:
Title:
Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2017-06-03
Release Date:
2018-06-06
Method Details:
Experimental Method:
Resolution:
2.05 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Vitamin D3 receptor
Mutations:deletion mutant(residues 165-211)
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Description:Nuclear receptor coactivator 2
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem. 60 8394 8406 (2017)
PMID: 28954197 DOI: 10.1021/acs.jmedchem.7b00819

Abstact

Vitamin D receptor (VDR) antagonists can be classified into two categories: the first category of VDR antagonists, which do not stabilize the helix 11-12, and the second category of antagonists, which destabilize the helix 6-7 region. To elucidate the mechanism underlying the first category antagonists by using the crystal structure, we designed and synthesized several VDR ligands with a p-hydroxyphenyl group at the C25-position. Of these, 22S-butyl-25-carbonyl analogue 5b and 25-di-p-hydoroxyphenyl analogues 6a,b showed strong antagonistic activity. We succeeded in cocrystallizing the ligand-binding domain of VDR complexed with 5b and found that the structure showed an alternative conformation of the helix 11-12 that explained the mechanism of the first category antagonists. Taking the present and previous studies together, we could elucidate the mechanisms underlying first and second categories antagonists based on individual crystal structures. This study provides significant insights into antagonism against not only VDR but also nuclear receptors.

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