Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions

J Med Chem. 2016 Jun 9;59(11):5555-61. doi: 10.1021/acs.jmedchem.6b00215. Epub 2016 May 24.

Abstract

BRPF1 plays a scaffolding role in transcription. We report on fragment screening by high-throughput docking to the BRPF1 bromodomain which resulted in six chemotypes with very favorable ligand efficiency (0.45-0.50 kcal/mol per non-hydrogen atom). Twenty crystal structures of BRPF1/ligand complexes show structural conservation in the acetyllysine binding site, common binding motifs, and unusual interactions (e.g., the replacement of a conserved water molecule). The structural information is useful for the design of chemical probes.

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry*
  • Binding Sites
  • Crystallography, X-Ray
  • DNA-Binding Proteins
  • Humans
  • Ligands*
  • Molecular Docking Simulation
  • Molecular Structure
  • Nuclear Proteins / chemistry*
  • Protein Domains
  • Protein Interaction Domains and Motifs
  • Water / chemistry

Substances

  • Adaptor Proteins, Signal Transducing
  • BRPF1 protein, human
  • DNA-Binding Proteins
  • Ligands
  • Nuclear Proteins
  • Water