BRD4 in complex with 138A

Experimental Data Snapshot

  • Resolution: 1.72 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

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Ligand Structure Quality Assessment 

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Discovery of Benzo[cd]indol-2(1H)-ones and Pyrrolo[4,3,2-de]quinolin-2(1H)-ones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain with Potential High Efficiency against Acute Gouty Arthritis.

Jiang, F.Hu, Q.Zhang, Z.Li, H.Li, H.Zhang, D.Li, H.Ma, Y.Xu, J.Chen, H.Cui, Y.Zhi, Y.Zhang, Y.Xu, J.Zhu, J.Lu, T.Chen, Y.

(2019) J Med Chem 62: 11080-11107

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01010
  • Primary Citation of Related Structures:  
    6JJ3, 6JJB

  • PubMed Abstract: 

    The bromodomain and extra-terminal domain (BET) family of proteins are readers which specifically recognize histone-acetylated lysine residues. Each BET bromodomain protein contains two highly homologous domains: the first bromodomain (BD1) and the second bromodomain (BD2). Pan-BET bromodomain inhibition is a potential therapy for various cancers and immune-inflammatory diseases, but only few reported inhibitors show selectivity within the BET family. Herein, we identified a series of benzo[ cd ]indol-2(1 H )-ones and pyrrolo[4,3,2- de ]quinolin-2(1 H )-ones with good selectivity for BET BD1. Through structure-based optimization, highly active and selective compounds are ultimately obtained. The representative compounds are the first reported inhibitors with selectivity more than 100-fold for BRD4(1) over BRD4(2). Among them, we further show that 68 (LT052) mediates BRD4/NF-κB/NLRP3 signaling inflammatory pathways with comparable protein expression and significantly improves symptoms of gout arthritis in a rat model. Therefore, selective pharmacological modulation of individual bromodomains could represent a strategy for the treatment of acute gouty arthritis.

  • Organizational Affiliation

    School of Sciences , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 4125Homo 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
BS6 (Subject of Investigation/LOI)
Query on BS6

Download Ideal Coordinates CCD File 
B [auth A]2-methoxy-N-[2-methyl-6-(4-methylpiperazin-1-yl)-3-oxidanylidene-2,7-diazatricyclo[^{4,12}]dodeca-1(12),4,6,8,10-pentaen-9-yl]benzenesulfonamide
C23 H25 N5 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
BS6 Binding MOAD:  6JJ3 IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.72 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.666α = 90
b = 46.918β = 90
c = 78.27γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references