9EYR image
Entry Detail
PDB ID:
9EYR
Keywords:
TRANSCRIPTION
Title:
VDR complex with gemini analog UG-480
Biological Source:
Source Organism:
Danio rerio, Homo sapiens
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2024-04-09
Release Date:
2024-06-19
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.56 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 65 2 2
9EYR validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:Vitamin D3 receptor A
Chain IDs:A
Chain Length:302
Number of Molecules:1
Biological Source:Danio rerio
UniProt ID:Q9PTN2 Pfam ID:PF00104 EC:2.3.1.48
Protein Blast
Polymer Type:polypeptide(L)
Description:Nuclear receptor coactivator 1
Chain IDs:B
Chain Length:15
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q15788 EC:2.3.1.48
Ligand Molecules
A1H75
Primary Citation
Design, Synthesis, and Biological Evaluation of New Type of Gemini Analogues with a Cyclopropane Moiety in Their Side Chain.
J.Med.Chem. 67 10386 10400 (2024)
PMID: 38858308 DOI: 10.1021/acs.jmedchem.4c00854

Abstact

We synthesized two new gemini analogues, UG-480 and UG-481, that incorporate a modified longer side chain containing a cyclopropane group. The evaluation of the bioactivities of the two gemini analogues indicated that the 17,20 threo (20S) compound, UG-480, is the most active one and is as active as 1,25(OH)2D3. Docking and molecular dynamics (MD) data showed that the compounds bind efficiently to vitamin D receptor (VDR) with UG-480 to form an energetically more favorable interaction with His397. Structural analysis indicated that whereas the UG-480 compound efficiently stabilizes the active VDR conformation, it induces conformational changes in the H6-H7 VDR region that are greater than those induced by the parental Gemini and that this is due to the occupancy of the secondary channel by its modified side chain.

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Primary Citation of related structures
9EYR