Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue

Structure

x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).

Ligands and binding sites

• 8J2 · propan-2-yl ~{N}-[(2~{S},4~{R})-6-(3-acetamidophenyl)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate · ligand · 4 copies · chains A, B, C, D
• SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, D

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

5 interfaces between chains.

• C–D · 296 Ų buried · 3 hydrogen bonds · protein-protein
• A–D · 240 Ų buried · 4 hydrogen bonds · protein-protein
• A–B · 224 Ų buried · 0 hydrogen bonds · protein-protein
• B–C · 213 Ų buried · 6 hydrogen bonds · protein-protein
• A–C · 148 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5N2L · Crystal structure of the second bromodomain of human BRD2 in complex with a… · the same entry in another collection · chain D against D, TM-score 1.00
• P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain C 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 5N2L · PDBe 5N2L · UniProt P25440