Crystal structure of human BRD9 bromodomain in complex with a PROTAC

Structure

x-ray diffraction · resolution 2.4 · 1 distinct chain · 63% helix, 0% strand (DSSP).

Ligands and binding sites

• GBW · (2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxidanylidene-2,7-naphthyridin-4-yl) phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl) phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · 2 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, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 516 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 6HM0 · Crystal structure of human BRD9 bromodomain in complex with a protac · the same entry in another collection · chain A against A, TM-score 1.00
• Q9H8M2 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 9 (Q9H8M2) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 Q9H8M2
• Elsewhere: RCSB PDB 6HM0 · PDBe 6HM0 · UniProt Q9H8M2