5N49

BRPF2 in complex with Compound 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains.

Bouche, L.Christ, C.D.Siegel, S.Fernandez-Montalvan, A.E.Holton, S.J.Fedorov, O.Ter Laak, A.Sugawara, T.Stockigt, D.Tallant, C.Bennett, J.Monteiro, O.Diaz-Saez, L.Siejka, P.Meier, J.Putter, V.Weiske, J.Muller, S.Huber, K.V.M.Hartung, I.V.Haendler, B.

(2017) J. Med. Chem. 60: 4002-4022

  • DOI: 10.1021/acs.jmedchem.7b00306
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bromodomains (BD) are readers of lysine acetylation marks present in numerous proteins associated with chromatin. Here we describe a dual inhibitor of the bromodomain and PHD finger (BRPF) family member BRPF2 and the TATA box binding protein-associat ...

    Bromodomains (BD) are readers of lysine acetylation marks present in numerous proteins associated with chromatin. Here we describe a dual inhibitor of the bromodomain and PHD finger (BRPF) family member BRPF2 and the TATA box binding protein-associated factors TAF1 and TAF1L. These proteins are found in large chromatin complexes and play important roles in transcription regulation. The substituted benzoisoquinolinedione series was identified by high-throughput screening, and subsequent structure-activity relationship optimization allowed generation of low nanomolar BRPF2 BD inhibitors with strong selectivity against BRPF1 and BRPF3 BDs. In addition, a strong inhibition of TAF1/TAF1L BD2 was measured for most derivatives. The best compound of the series was BAY-299, which is a very potent, dual inhibitor with an IC50 of 67 nM for BRPF2 BD, 8 nM for TAF1 BD2, and 106 nM for TAF1L BD2. Importantly, no activity was measured for BRD4 BDs. Furthermore, cellular activity was evidenced using a BRPF2- or TAF1-histone H3.3 or H4 interaction assay.


    Organizational Affiliation

    Drug Discovery, Bayer AG , M├╝llerstrasse 178, 13353 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 1
A, B
135Homo sapiensMutation(s): 0 
Gene Names: BRD1 (BRL, BRPF2)
Find proteins for O95696 (Homo sapiens)
Go to Gene View: BRD1
Go to UniProtKB:  O95696
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8LW
Query on 8LW

Download SDF File 
Download CCD File 
B
2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione
C22 H17 N3 O3
WNTOXMAGPDYDCR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8LWIC50: 60 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.556α = 90.00
b = 56.983β = 90.00
c = 102.340γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references