5ZWI image
Deposition Date 2018-05-15
Release Date 2018-07-18
Last Version Date 2024-03-27
Entry Detail
PDB ID:
5ZWI
Keywords:
Title:
Interaction between Vitamin D receptor (VDR) and a ligand having a dienone group
Biological Source:
Source Organism:
Rattus norvegicus (Taxon ID: 10116)
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Vitamin D3 receptor
Gene (Uniprot):Vdr
Mutations:165-211 deletion
Chain IDs:A
Chain Length:271
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:13-meric peptide from DRIP205 NR2 BOX peptide
Chain IDs:B (auth: C)
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Identification of the Histidine Residue in Vitamin D Receptor That Covalently Binds to Electrophilic Ligands
J. Med. Chem. 61 6339 6349 (2018)
PMID: 29936834 DOI: 10.1021/acs.jmedchem.8b00774

Abstact

We designed and synthesized vitamin D analogues with an electrophile as covalent modifiers for the vitamin D receptor (VDR). Novel vitamin D analogues 1-4 have an electrophilic enone group at the side chain for conjugate addition to His301 or His393 in the VDR. All compounds showed specific VDR-binding potency and agonistic activity. Covalent bond formations of 1-4 with the ligand-binding domain (LBD) of VDR were evaluated by electrospray ionization mass spectrometry. All compounds were shown to covalently bind to the VDR-LBD, and the abundance of VDR-LBD corresponding conjugate adducts of 1-4 increased with incubation time. Enone compounds 1 and 2 showed higher reactivity than the ene-ynone 3 and dienone 4 compounds. Furthermore, we successfully obtained cocrystals of VDR-LBD with analogues 1-4. X-ray crystallographic analysis showed a covalent bond with His301 in VDR-LBD. We successfully synthesized vitamin D analogues that form a covalent bond with VDR-LBD.

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Primary Citation of related structures