Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-in-1

Structure

x-ray diffraction · 3 distinct chains · 69% 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, C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–C · 801 Ų buried · 11 hydrogen bonds · protein-protein
• A–D · 457 Ų buried · 13 hydrogen bonds · protein-protein
• A–B · 433 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 289 Ų buried · 2 hydrogen bonds · protein-protein
• C–D · 34 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 7LBT · Crystal structure of the second bromodomain (BD2) of human BRD3 bound to ERK5-IN-1 · the same entry in another collection · chain D against D, TM-score 1.00
• Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · a predicted model of the same protein · chain B 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 Q15059
• Elsewhere: RCSB PDB 7LBT · PDBe 7LBT · UniProt Q15059