6T2M image
Deposition Date 2019-10-09
Release Date 2020-08-26
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6T2M
Keywords:
Title:
VDR-ZK168281 complex
Biological Source:
Source Organism:
Danio rerio (Taxon ID: 7955)
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 65 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Vitamin D3 receptor A
Gene (Uniprot):vdra
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Danio rerio
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nuclear receptor coactivator 1
Gene (Uniprot):NCOA1
Chain IDs:B
Chain Length:15
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural Analysis of VDR Complex with ZK168281 Antagonist.
J.Med.Chem. 63 9457 9463 (2020)
PMID: 32787090 DOI: 10.1021/acs.jmedchem.0c00656

Abstact

Vitamin D receptor (VDR) antagonists prevent the VDR activation function helix 12 from folding into its active conformation, thus affecting coactivator recruitment and antagonizing the transcriptional regulation induced by 1α,25-dihydroxyvitamin D3. Here, we report the crystal structure of the zebrafish VDR ligand-binding domain in complex with the ZK168281 antagonist, revealing that the ligand prevents optimal folding of the C-terminal region of VDR. This interference was confirmed by hydrogen-deuterium exchange mass spectrometry (HDX-MS) in solution.

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Primary Citation of related structures