Crystal structure of the first bromodomain (BD1) of human BRD4 bound to BI9564

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

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This is version 1.2 of the entry. See complete history


Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.

Karim, R.M.Chan, A.Zhu, J.Y.Schonbrunn, E.

(2020) J Med Chem 63: 3227-3237

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01980
  • Primary Citation of Related Structures:  
    6PPA, 6UZF, 6V0Q, 6V0S, 6V0U, 6V0X, 6V14, 6V16, 6V17, 6V1B, 6V1E, 6V1F, 6V1H, 6V1K, 6V1L, 6V1U

  • PubMed Abstract: 

    Inhibition of the bromodomain containing protein 9 (BRD9) by small molecules is an attractive strategy to target mutated SWI/SNF chromatin-remodeling complexes in cancer. However, reported BRD9 inhibitors also inhibit the closely related bromodomain-containing protein 7 (BRD7), which has different biological functions. The structural basis for differential potency and selectivity of BRD9 inhibitors is largely unknown because of the lack of structural information on BRD7. Here, we biochemically and structurally characterized diverse inhibitors with varying degrees of potency and selectivity for BRD9 over BRD7. Novel cocrystal structures of BRD7 liganded with new and previously reported inhibitors of five different chemical scaffolds were determined alongside BRD9 and BRD4. We also report the discovery of first-in-class dual bromodomain-kinase inhibitors outside the bromodomain and extraterminal family targeting BRD7 and BRD9. Combined, the data provide a new framework for the development of BRD7/9 inhibitors with improved selectivity or additional polypharmacologic properties.

  • Organizational Affiliation

    Department of Drug Discovery, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, Florida 33612, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
PHAROS:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5U6 (Subject of Investigation/LOI)
Query on 5U6

Download Ideal Coordinates CCD File 
B [auth A]4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one
C20 H23 N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
5U6 Binding MOAD:  6V1L Kd: 418 (nM) from 1 assay(s)
BindingDB:  6V1L Kd: min: 1.00e+4, max: 2.00e+4 (nM) from 2 assay(s)
IC50: 1.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.94α = 90
b = 51.29β = 90
c = 52.51γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description