Structural analysis and biological activities of BXL0124, a gemini analog of vitamin D

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Ligands and binding sites

• 6VH · (1~{R},3~{S},5~{Z})-5-[2-[(1~{R},3~{A}~{S},7~{A}~{R})-7~{A}-methyl-1-[(6~{R})-1,1,1-tris(fluoranyl)-10-methyl-2,10-bis(oxidanyl)-2-(trifluoromethyl)undeca-3, 8-diyn-6-yl]-2,3,3~{A},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 567 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 5LGA · Structural analysis and biological activities of BXL0124, a Gemini analog of Vitamin D · the same entry in another collection · chain A against A, TM-score 1.00
• Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9PTN2
• Elsewhere: RCSB PDB 5LGA · PDBe 5LGA · UniProt Q9PTN2