Crystal structure of the second bromodomain (BD2) of human BRD2 bound to LRRK2-in-1

Structure

x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).

Ligands and binding sites

• 4K4 · 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one · ligand · 3 copies · chains A, B
• BU1 · 1,4-butanediol · additive · 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, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 881 Ų buried · 9 hydrogen bonds · protein-protein

Compared structures

• 7L9K · Crystal structure of the second bromodomain (BD2) of human BRD2 bound to LRRK2-IN-1 · the same entry in another collection · chain A against A, TM-score 1.00
• P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P25440
• Elsewhere: RCSB PDB 7L9K · PDBe 7L9K · UniProt P25440