Crystal structure of BRD4 in complex with isoliquiritigenin in the absence of DMSO

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.

Yokoyama, T.Matsumoto, K.Ostermann, A.Schrader, T.E.Nabeshima, Y.Mizuguchi, M.

(2019) FEBS J 286: 1656-1667

  • DOI: https://doi.org/10.1111/febs.14736
  • Primary Citation of Related Structures:  
    6AJV, 6AJW, 6AJX, 6AJY, 6AJZ

  • PubMed Abstract: 

    Bromodomain-containing protein 4 (BRD4) recognizes the acetylated lysine of histone H4 via its bromodomains, leading to the recruitment of positive transcription elongation factor b. Small molecules that inhibit BRD4 have potential as anticancer agents by leading to the downregulation of specific oncogenes. Using X-ray crystallographic screening, we identified the BRD4 inhibitory activity of isoliquiritigenin (ISL), a natural chalcone found in licorice. Structural analysis revealed that ISL bound to BRD4 with a novel binding mode and squeezed out one of the six conserved water molecules that form a strong hydrogen bond network. The thermodynamic analysis revealed that the binding of ISL is enthalpy driven, suggesting that strong hydrogen bonds would compensate for the desolvation penalty. Neutron protein crystallography further suggested that the favorable binding enthalpy originates from the stabilization and optimization of the hydrogen bond network of the conserved water molecules. Here, we describe the novelty and potential of ISL as a template for new BRD4 inhibitors.

  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4135Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
HCC Binding MOAD:  6AJX Kd: 9100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.83α = 90
b = 46.875β = 90
c = 78.511γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations