Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-in-1

Structure

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

Ligands and binding sites

• VYJ · 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one · ligand · 4 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 327 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 7K6G · Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-IN-1 · 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 7K6G · PDBe 7K6G · UniProt O60885