2ZXN image
Entry Detail
PDB ID:
2ZXN
Keywords:
Title:
A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2009-01-04
Release Date:
2009-02-17
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Vitamin D3 receptor
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Description:Mediator of RNA polymerase II transcription subunit 1
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:
Ligand Molecules
Primary Citation
A New Class of Vitamin D Analogues that Induce Structural Rearrangement of the Ligand-Binding Pocket of the Receptor
J.Med.Chem. 52 1438 1449 (2009)
PMID: 19193059 DOI: 10.1021/jm8014348

Abstact

To identify novel vitamin D receptor (VDR) ligands that induce a novel architecture within the ligand-binding pocket (LBP), we have investigated eight 22-butyl-1alpha,24-dihydroxyvitamin D(3) derivatives (3-10), all having a butyl group as the branched alkyl side chain. We found that the 22S-butyl-20-epi-25,26,27-trinorvitamin D derivative 5 was a potent VDR agonist, whereas the corresponding compound 4 with the natural configuration at C(20) was a potent VDR antagonist. Analogues with the full vitamin D(3) side chain were less potent agonist, and whether they were agonists or antagonists depended on the 24-configuration. X-ray crystal structures demonstrated that the VDR-LBD accommodating the potent agonist 5 has an architecture wherein the lower side and the helix 11 side of the LBP is simply expanded relative to the canonical active-VDR situation; in contrast, the potent antagonist 4 induces an extra cavity to accommodate the branched moiety. This is the first report of a VDR antagonist that generates a new cavity to alter the canonical pocket structure of the ligand occupied VDR.

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Primary Citation of related structures