Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 22

Experimental Data Snapshot

  • Resolution: 2.83 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia.

Jiang, W.Hou, Q.Xu, H.Yang, K.Wang, X.Zhang, K.Zeng, Y.Li, W.Wang, B.Luo, G.Zhao, X.Shen, H.Xu, Y.Wu, X.

(2024) J Med Chem 67: 1513-1532

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02104
  • Primary Citation of Related Structures:  
    8WXY, 8WY3, 8WY7, 8WYG

  • PubMed Abstract: 

    Bromodomain-selective BET inhibition has emerged as a promising strategy to improve the safety profiles of pan -BET inhibitors. Herein, we report the discovery of potent phenoxyaryl pyridones as highly BD2-selective BET inhibitors. Compound 23 (IC 50 = 2.9 nM) exhibited a comparable BRD4 BD2 inhibitory activity relative to 10 (IC 50 = 1.0 nM) and remarkably improved selectivity over BRD4 BD1 ( 23 : 2583-fold; 10 : 344-fold). This lead compound significantly inhibited the proliferation of acute myeloid leukemia (AML) cell lines through induction of G0/G1 arrest and apoptosis in vitro . Excellent in vivo antitumor efficacy with 23 was achieved in an MV;411 mouse xenograft model. Pleasingly, compound 23 (hERG IC 50 > 30 μM) mitigated the inhibition of the human ether-à-go-go-related gene (hERG) ion channel compared with 10 (hERG IC 50 = 2.8 μM). This work provides a promising BD2-selective lead for the development of more effective and safe BET inhibitors as anticancer agents.

  • Organizational Affiliation

    Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4
A, B, C
141Homo 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
XHN (Subject of Investigation/LOI)
Query on XHN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
C31 H38 F N3 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.83 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.15α = 90
b = 140.15β = 90
c = 134.299γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22307116

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references