Crystal structure of the first bromodomain (BD1) of human brdt bound to LRRK2-in-1

Structure

x-ray diffraction · 1 distinct chain · 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 · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 10 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 809 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 7LEM · Crystal structure of the first bromodomain (BD1) of human BRDT bound to LRRK2-IN-1 · the same entry in another collection · chain A against A, TM-score 1.00
• Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · 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 Q58F21
• Elsewhere: RCSB PDB 7LEM · PDBe 7LEM · UniProt Q58F21