5O5F

Crystal structure of the human BRPF1 bromodomain in complex with BZ038


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.302 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based discovery of selective BRPF1 bromodomain inhibitors.

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

(2018) Eur J Med Chem 155: 337-352

  • DOI: 10.1016/j.ejmech.2018.05.037
  • Primary Citation of Related Structures:  

  • 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 id ...

    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.,Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland. Electronic address: caflisch@bioc.uzh.ch.,Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peregrin
A
116Homo sapiensMutation(s): 0 
Gene Names: BRPF1 (BR140)
Find proteins for P55201 (Homo sapiens)
Go to Gene View: BRPF1
Go to UniProtKB:  P55201
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9LT
Query on 9LT

Download SDF File 
Download CCD File 
A
1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide
C22 H20 F N5 O3
ORFTXHBAJDABTM-GOSISDBHSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.302 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.175 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.765α = 90.00
b = 60.765β = 90.00
c = 63.516γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-06-01 
  • Released Date: 2018-06-13 
  • Deposition Author(s): Zhu, J., Caflisch, A.

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references