Crystal structure of the BCL6 btb domain in complex with oicr-12694

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).

Ligands and binding sites

• YN7 · 5-{(5S)-1-[2-({3-chloro-6-[(2S)-2,4-dimethylpiperazin-1-yl]-2-fluoropyridin-4-yl}amino)-2-oxoethyl]-4-oxo-4, 6,7,8-tetrahydro-1H-dipyrrolo[1,2-A:2',3'-d]pyrimidin-3-yl}-3,4-difluoro-2-hydroxybenzamide · ligand · 2 copies · chains A, B
• UNX · Unknown atom or ion · ion · 4 copies · chains A, B
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1741 Ų buried · 18 hydrogen bonds · protein-protein

Compared structures

• 7LWG · Crystal structure of the BCL6 BTB domain in complex with OICR-12694 · the same entry in another collection · chain A against A, TM-score 1.00
• P41182 · AlphaFold monomer V2.0 prediction for B-cell lymphoma 6 protein (P41182) · a predicted model of the same protein · chain A against A, TM-score 0.32

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 P41182
• Elsewhere: RCSB PDB 7LWG · PDBe 7LWG · UniProt P41182