Crystal structure of the first bromodomain of human brdt in complex with volasertib

Structure

x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).

Ligands and binding sites

• IBI · N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 11 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, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 858 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 5VBR · CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRDT IN COMPLEX WITH Volasertib · 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 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 Q58F21
• Elsewhere: RCSB PDB 5VBR · PDBe 5VBR · UniProt Q58F21