Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with bivalent inhibitor gxh-II-083

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 0% strand (DSSP).

Ligands and binding sites

• XR4 · N,N'-[(1,19-dioxo-4,7,10,13,16-pentaoxanonadecane-1,19-diyl)di(piperidine-1,4-diyl)]bis(4-{[4-({3-[(tert-butylsulfonyl)amino]-4-chlorophenyl}amino)-5-methylpyrimidin-2-yl]amino}-2-fluorobenzamide) · ligand · chains A, B
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, B

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 · 430 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 7L9M · Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with bivalent… · the same entry in another collection · chain A against A, TM-score 1.00
• O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O60885
• Elsewhere: RCSB PDB 7L9M · PDBe 7L9M · UniProt O60885