9GY8 image
Deposition Date 2024-10-01
Release Date 2024-12-11
Last Version Date 2024-12-25
Entry Detail
PDB ID:
9GY8
Keywords:
Title:
Vitamin D Receptor complex with Sila-A
Biological Source:
Source Organism:
Danio rerio (Taxon ID: 7955)
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 65 2 2
Macromolecular Entities
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
Polymer Type:polypeptide(L)
Molecule:Nuclear receptor coactivator 2
Gene (Uniprot):NCOA2
Chain IDs:B
Chain Length:13
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
First Sila-Vitamin D Analogues: Design, Synthesis, Structural Analysis and Biological Activity.
J.Med.Chem. 67 21505 21519 (2024)
PMID: 39610329 DOI: 10.1021/acs.jmedchem.4c02404

Abstact

The incorporation of silicon bioisosteres into pharmacological structures has been used as a strategy to improve the therapeutic potential of drugs. However, no secosteroidal silicon-containing VDR ligands have been developed. Here we report the design, synthesis, and biological activity of six analogues of the natural hormone 1,25-dihydroxyvitamin D3 (1,25D3), which incorporate a silicon atom as a side chain-C25 isostere. The analogues were synthesized by the Wittig-Horner approach starting from Inhoffen-Lythgoe diol. The crystal structures of the complexes formed by the sila-analogues with the ligand binding domain of VDR revealed additional interactions of the sila-containing side chains that stabilize the VDR active conformation. These sila-analogues show similar VDR binding and transcriptional activity in comparison with the natural hormone 1,25D3, but with significantly less hypercalcemic activity. The new analogues, when combined with chemotherapy, significantly decrease cell proliferation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures