Crystal structure of the human BRPF1 bromodomain complexed with BZ054 in space group C2

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

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Structure-based discovery of selective BRPF1 bromodomain inhibitors.

Zhu, J.Zhou, C.Caflisch, A.

(2018) Eur J Med Chem 155: 337-352

  • DOI: https://doi.org/10.1016/j.ejmech.2018.05.037
  • Primary Citation of Related Structures:  
    5MWG, 5MWH, 5MWZ, 5O4S, 5O4T, 5O55, 5O5A, 5O5F, 5O5H, 5OV8, 5OWA, 6EKQ

  • PubMed Abstract: 

    Bromodomain and plant homeodomain (PHD) finger containing protein 1 (BRPF1) is a member of subfamily IV of the human bromodomains. Experimental evidence suggests that BRPF1 is involved in leukemia. In a previous high-throughput docking campaign we identified several chemotypes targeting the BRPF1 bromodomain. Here, pharmacophore searches using the binding modes of two of these chemotypes resulted in two new series of ligands of the BRPF1 bromodomain. The 2,3-dioxo-quinoxaline 21 exhibits a 2-μM affinity for the BRPF1 bromodomain in two different competition binding assays, and more than 100-fold selectivity for BRPF1 against other members of subfamily IV and representatives of other subfamilies. Cellular activity is confirmed by a viability assay in a leukemia cell line. Isothermal titration calorimetry measurements reveal enthalpy-driven binding for compounds 21, 26 (K D  = 3 μM), and the 2,4-dimethyl-oxazole derivative 42 (K D  = 10 μM). Multiple molecular dynamics simulations and a dozen co-crystal structures at high resolution provide useful information for further optimization of affinity for the BRPF1 bromodomain.

  • Organizational Affiliation

    Department of Pathology, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Pudong District, Shanghai, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
116Homo sapiensMutation(s): 0 
Gene Names: BRPF1BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens)
Explore P55201 
Go to UniProtKB:  P55201
PHAROS:  P55201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55201
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
B0H BindingDB:  6EKQ Kd: min: 3500, max: 1.09e+4 (nM) from 2 assay(s)
IC50: 3.06e+4 (nM) from 1 assay(s)
Binding MOAD:  6EKQ Kd: 1.09e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.208α = 90
b = 57.784β = 108.66
c = 70.446γ = 90
Software Package:
Software NamePurpose
Mantiddata reduction
ADDREFdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release