Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.58 kDa 
• Atom Count: 1294 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

4BW2

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

• PDB DOI: 10.2210/pdb4BW2/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-29 Released: 2013-09-11 
• Deposition Author(s): Chung, C., Mirguet, O., Lamotte, Y., Bamborough, P., Delannee, D., Bouillot, A., Gellibert, F., Krysa, G., Lewis, A., Witherington, J., Huet, P., Dudit, Y., Trottet, L., Nicodeme, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.222 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

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

• PubMed: 24000170 
• DOI: 10.1002/cmdc.201300259
• Primary Citation of Related Structures:  
  4BW1, 4BW2, 4BW3, 4BW4


• 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, 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.

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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). [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTH	C [auth A]	4-((2-(TERT-BUTYL)PHENYL)AMINO)-7-(3,5-dimethylisoxazol-4-yl)-1,8-naphthyridine-3-carboxylic acid C24 H24 N4 O3 PTXRSHPWCLHNBN-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UTH	Binding MOAD:  4BW2	IC50: 6310 (nM) from 1 assay(s)
	PDBBind:  4BW2	IC50: 6310 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.222 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.93	α = 90
b = 47.86	β = 90
c = 61.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-29 
• Released Date: 2013-09-11 
Deposition Author(s): Chung, C., Mirguet, O., Lamotte, Y., Bamborough, P., Delannee, D., Bouillot, A., Gellibert, F., Krysa, G., Lewis, A., Witherington, J., Huet, P., Dudit, Y., Trottet, L., Nicodeme, E.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references