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

Structure

x-ray diffraction · 4 distinct chains · 70% 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, C, D, B
• CL · Chloride ion · ion · chains B
• EDO · 1,2-ethanediol · additive · chains A, C

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

Pockets

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

Interfaces

5 interfaces between chains.

• B–D · 650 Ų buried · 9 hydrogen bonds · protein-protein
• A–C · 531 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 417 Ų buried · 0 hydrogen bonds · protein-protein
• A–B · 69 Ų buried · 0 hydrogen bonds · protein-protein
• C–D · 42 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 7LEK · Crystal structure of the second bromodomain (BD2) of human BRDT bound to ERK5-IN-1 · the same entry in another collection · chain D against D, TM-score 1.00
• Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 7LEK · PDBe 7LEK · UniProt Q58F21