Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-052

Experimental Data Snapshot

  • Resolution: 1.82 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

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This is version 1.3 of the entry. See complete history


Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity.

Guan, X.Cheryala, N.Karim, R.M.Chan, A.Berndt, N.Qi, J.Georg, G.I.Schonbrunn, E.

(2022) J Med Chem 65: 10441-10458

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00453
  • Primary Citation of Related Structures:  
    7L9M, 7LA9, 7MR5, 7MR6, 7MR7, 7MR9, 7MRA, 7MRB, 7MRC, 7MRD, 7MRG, 7MRH, 8CZA

  • PubMed Abstract: 

    Bromodomain and extraterminal domain (BET) proteins are important regulators of gene transcription and chromatin remodeling. BET family members BRD4 and BRDT are validated targets for cancer and male contraceptive drug development, respectively. Due to the high structural similarity of the acetyl-lysine binding sites, most reported inhibitors lack intra-BET selectivity. We surmised that protein-protein interactions induced by bivalent inhibitors may differ between BRD4 and BRDT, conferring an altered selectivity profile. Starting from nonselective monovalent inhibitors, we developed cell-active bivalent BET inhibitors with increased activity and selectivity for BRDT. X-ray crystallographic and solution studies revealed unique structural states of BRDT and BRD4 upon interaction with bivalent inhibitors. Varying spacer lengths and symmetric vs unsymmetric connections resulted in the same dimeric states, whereas different chemotypes induced different dimers. The findings indicate that the increased intra-BET selectivity of bivalent inhibitors is due to the differential plasticity of BET bromodomains upon inhibitor-induced dimerization.

  • Organizational Affiliation

    Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, Minneapolis, Minnesota 55414, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B
127Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
GTEx:  ENSG00000141867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60885
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZMS (Subject of Investigation/LOI)
Query on ZMS

Download Ideal Coordinates CCD File 
C [auth A]N,N'-{oxybis[(ethane-2,1-diyl)oxy(1-oxoethane-2,1-diyl)piperidine-1,4-diyl]}bis{4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluorobenzamide}
C62 H76 Cl2 F2 N14 O11 S2
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.82 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.08α = 99.95
b = 39.71β = 104.45
c = 57.18γ = 89.99
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States1U54HD093540

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description