Crystal structure of TRIM24 phd-bromodomain complexed with N-{6-[3- (BENZYLOXY)PHENOXY]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3- benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide (7B)

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 2% strand (DSSP).

Ligands and binding sites

• 4BJ · N-{6-[3-(benzyloxy)phenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}-3,4-dimethoxybenzenesulfonamide · ligand · 2 copies · chains A, B
• ZN · Zinc ion · metal · 4 copies · chains A, B
• SO4 · Sulfate ion · ion · 2 copies · chains B
• GOL · Glycerol · additive · 4 copies · 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 · 666 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 4YBM · Crystal structure of TRIM24 PHD-bromodomain complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
• O15164 · AlphaFold monomer V2.0 prediction for transcription intermediary factor 1-alpha (O15164) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O15164
• Elsewhere: RCSB PDB 4YBM · PDBe 4YBM · UniProt O15164