Crystal structure of BRD4 first bromodomain in complex with sgc-CBP30 chemical probe

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 0% strand (DSSP).

Ligands and binding sites

• 2LO · 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole · ligand · 3 copies · chains A, B, C
• EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C

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

3 interfaces between chains.

• A–B · 335 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 332 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 36 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 5BT4 · Crystal structure of BRD4 first bromodomain in complex with SGC-CBP30 chemical probe · the same entry in another collection · chain A against A, TM-score 1.00
• O60885 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 4 (O60885) · 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 O60885
• Elsewhere: RCSB PDB 5BT4 · PDBe 5BT4 · UniProt O60885