Crystal structure of the first bromodomain (BD1) of human brdt bound to gxh-II-052

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 0% strand (DSSP).

Ligands and binding sites

• ZMS · N,N'-{oxybis[(ethane-2,1-diyl)oxy(1-oxoethane-2,1-diyl)piperidine-1,4-diyl]}bis{4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluorobenzamide} · ligand · chains A, B
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
• DMS · Dimethyl sulfoxide · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 266 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 7MRC · Crystal structure of the first bromodomain (BD1) of human BRDT bound to GXH-II-052 · the same entry in another collection · chain A against A, TM-score 1.00
• Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q58F21
• Elsewhere: RCSB PDB 7MRC · PDBe 7MRC · UniProt Q58F21