Crystal structure of the bromodomain of human BRD9 bound to TP472

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report

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This is version 1.3 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 9123Homo sapiensMutation(s): 0 
Gene Names: BRD9UNQ3040/PRO9856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8M2 (Homo sapiens)
Explore Q9H8M2 
Go to UniProtKB:  Q9H8M2
GTEx:  ENSG00000028310 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H8M2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QMG (Subject of Investigation/LOI)
Query on QMG

Download Ideal Coordinates CCD File 
B [auth A]3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide
C20 H19 N3 O2
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
QMG BindingDB:  6V14 Kd: min: 32, max: 82 (nM) from 3 assay(s)
Binding MOAD:  6V14 Kd: 82 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.27α = 104.1
b = 33.86β = 102.1
c = 37.68γ = 105.91
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: 2020-07-01
    Changes: Data collection
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description