5E3D image
Deposition Date 2015-10-02
Release Date 2016-05-25
Last Version Date 2024-01-10
Entry Detail
PDB ID:
5E3D
Keywords:
DNA BINDING PROTEIN
Title:
Crystal structure of the human BRPF1 bromodomain in complex with SEED7
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.71 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 32 2 1
5E3D validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peregrin
Gene (Uniprot):BRPF1
Chain IDs:A
Chain Length:116
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P55201 Pfam ID:PF00439
Ligand Molecules
5JL
NO3
Primary Citation
Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions.
J.Med.Chem. 59 5555 5561 (2016)
PMID: 27167503 DOI: 10.1021/acs.jmedchem.6b00215

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5E3D