6JJ3

BRD4 in complex with 138A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report



Literature

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: 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 s ...

    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

    State Key Laboratory of Natural Medicines , China Pharmaceutical University , 24 Tongjiaxiang , Nanjing 210009 , P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A125Homo sapiensMutation(s): 0 
Gene Names: BRD4HUNK1
Find proteins for O60885 (Homo sapiens)
Explore O60885 
Go to UniProtKB:  O60885
NIH Common Fund Data Resources
PHAROS  O60885
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BS6
Query on BS6

Download CCD File 
A
2-methoxy-N-[2-methyl-6-(4-methylpiperazin-1-yl)-3-oxidanylidene-2,7-diazatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaen-9-yl]benzenesulfonamide
C23 H25 N5 O4 S
OCFSAAGNZRGIDJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
TRUNCATEdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release