Crystal structure of the first bromodomain (BD1) of human brdt bound to gxh-IV-075

Structure

x-ray diffraction · 6 distinct chains · 63% helix, 0% strand (DSSP).

Ligands and binding sites

• ZN1 · 4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl) amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluoro-N-[1-(14-{3-[(2-{3-fluoro-4-[(piperidin-4-yl) carbamoyl]anilino}-5-methylpyrimidin-4-yl)amino]-5-[(2-methylpropane-2-sulfonyl)amino]phenyl}-14-oxo-4,7, 10-trioxa-13-azatetradecanan-1-oyl)piperidin-4-yl]benzamide · ligand · 3 copies · chains A, B, C, D, E, F
• NA · Sodium ion · metal · 2 copies · chains C, D

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

Pockets

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

Interfaces

5 interfaces between chains.

• B–F · 577 Ų buried · 1 hydrogen bond · protein-protein
• C–D · 279 Ų buried · 1 hydrogen bond · protein-protein
• A–B · 265 Ų buried · 2 hydrogen bonds · protein-protein
• E–F · 262 Ų buried · 1 hydrogen bond · protein-protein
• B–D · 156 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 8CZA · Crystal structure of the first bromodomain (BD1) of human BRDT bound to GXH-IV-075 · the same entry in another collection · chain F against F, TM-score 1.00
• Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · a predicted model of the same protein · chain C 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 8CZA · PDBe 8CZA · UniProt Q58F21