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 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.7b00306
  • Primary Citation of Related Structures:  
    5MG2, 5N49

  • 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-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 IC 50 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 , Müllerstrasse 178, 13353 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 1
A, B
135Homo sapiensMutation(s): 0 
Gene Names: BRD1BRLBRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens)
Explore O95696 
Go to UniProtKB:  O95696
PHAROS:  O95696
GTEx:  ENSG00000100425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95696
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8LW
Query on 8LW

Download Ideal Coordinates CCD File 
C [auth B]2-(1,3,6-trimethyl-2-oxidanylidene-benzimidazol-5-yl)benzo[de]isoquinoline-1,3-dione
C22 H17 N3 O3
WNTOXMAGPDYDCR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.556α = 90
b = 56.983β = 90
c = 102.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references
  • Version 1.2: 2017-05-24
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Structure summary