4BW1

The first bromodomain of human BRD4 in complex with 3,5 dimethylisoxaxole ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Naphthyridines as Novel Bet Family Bromodomain Inhibitors.

Mirguet, O.Lamotte, Y.Chung, C.Bamborough, P.Delannee, D.Bouillot, A.Gellibert, F.Krysa, G.Lewis, A.Witherington, J.Huet, P.Dudit, Y.Trottet, L.Nicodeme, E.

(2014) Chemmedchem 9: 589

  • DOI: 10.1002/cmdc.201300259
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bromodomains (BRDs) are small protein domains found in a variety of proteins that recognize and bind to acetylated histone tails. This binding affects chromatin structure and facilitates the localisation of transcriptional complexes to specific genes ...

    Bromodomains (BRDs) are small protein domains found in a variety of proteins that recognize and bind to acetylated histone tails. This binding affects chromatin structure and facilitates the localisation of transcriptional complexes to specific genes, thereby regulating epigenetically controlled processes including gene transcription and mRNA elongation. Inhibitors of the bromodomain and extra-terminal (BET) proteins BRD2-4 and T, which prevent bromodomain binding to acetyl-modified histone tails, have shown therapeutic promise in several diseases. We report here the discovery of 1,5-naphthyridine derivatives as potent inhibitors of the BET bromodomain family with good cell activity and oral pharmacokinetic parameters. X-ray crystal structures of naphthyridine isomers have been solved and quantum mechanical calculations have been used to explain the higher affinity of the 1,5-isomer over the others. The best compounds were progressed in a mouse model of inflammation and exhibited dose-dependent anti-inflammatory pharmacology.


    Organizational Affiliation

    Centre de Recherches François Hyafil, GlaxoSmithKline R&D, 25 Avenue du Québec, 91140 Villebon-sur-Yvette (France); Current address: Institut de Recherches Servier, 11 Rue des Moulineaux, 92150 Suresnes (France). oliviermirguet@yahoo.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BROMODOMAIN-CONTAINING PROTEIN 4
A
127Homo sapiensMutation(s): 0 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S5B
Query on S5B

Download SDF File 
Download CCD File 
A
4-[(2-tert-butylphenyl)amino]-7-(3,5-dimethyl-1,2-oxazol-4-yl)quinoline-3-carboxylic acid
C25 H25 N3 O3
OWUQUQCSBQATFQ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S5BIC50: 1258.9 nM (99) BINDINGDB
S5BIC50: 1260 nM BINDINGMOAD
S5BIC50: 1260 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.970α = 90.00
b = 47.810β = 90.00
c = 61.910γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references, Source and taxonomy