3P5O

Crystal Structure of the First Bromodomain of Human Brd4 in complex with IBET inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Suppression of inflammation by a synthetic histone mimic

Nicodeme, E.Jeffrey, K.L.Schaefer, U.Beinke, S.Dewell, S.Chung, C.Chandwani, R.Marazzi, I.Wilson, P.Coste, H.White, J.Kirilovsky, J.Rice, C.M.Lora, J.M.Prinjha, R.K.Lee, K.Tarakhovsky, A.

(2010) Nature 468: 1119-1123

  • DOI: 10.1038/nature09589
  • Primary Citation of Related Structures:  
    3P5O

  • PubMed Abstract: 
  • Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defence, is frequently deleterious to the host due to the exaggerated production of inflammatory ...

    Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defence, is frequently deleterious to the host due to the exaggerated production of inflammatory proteins. The scope of inflammatory responses reflects the activation state of signalling proteins upstream of inflammatory genes as well as signal-induced assembly of nuclear chromatin complexes that support mRNA expression. Recognition of post-translationally modified histones by nuclear proteins that initiate mRNA transcription and support mRNA elongation is a critical step in the regulation of gene expression. Here we present a novel pharmacological approach that targets inflammatory gene expression by interfering with the recognition of acetylated histones by the bromodomain and extra terminal domain (BET) family of proteins. We describe a synthetic compound (I-BET) that by 'mimicking' acetylated histones disrupts chromatin complexes responsible for the expression of key inflammatory genes in activated macrophages, and confers protection against lipopolysaccharide-induced endotoxic shock and bacteria-induced sepsis. Our findings suggest that synthetic compounds specifically targeting proteins that recognize post-translationally modified histones can serve as a new generation of immunomodulatory drugs.


    Organizational Affiliation

    Centre de Recherche GSK, 27 Avenue du Québec, 91140 Villebon Sur Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain-containing protein 4A127Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EAM
Query on EAM

Download CCD File 
A
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide
C22 H22 Cl N5 O2
AAAQFGUYHFJNHI-SFHVURJKSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EAMIC50:  156   nM  BindingDB
EAMIC50:  190   nM  BindingDB
EAMKi:  23   nM  BindingDB
EAMIC50:  260   nM  BindingDB
EAMIC50:  20   nM  BindingDB
EAMIC50:  36.099998474121094   nM  BindingDB
EAMKi:  32   nM  BindingDB
EAMKi:  39   nM  BindingDB
EAMKd:  48   nM  BindingDB
EAMKd:  49   nM  BindingDB
EAMKi:  46   nM  BindingDB
EAMKd:  37   nM  BindingDB
EAMIC50:  36   nM  BindingDB
EAMIC50:  40   nM  BindingDB
EAMIC50:  630   nM  BindingDB
EAMIC50:  631   nM  BindingDB
EAMKd:  65   nM  BindingDB
EAMIC50:  740   nM  BindingDB
EAMKd :  50.5   nM  PDBBind
EAMKd:  99   nM  BindingDB
EAMKd:  95   nM  BindingDB
EAMIC50:  61   nM  BindingDB
EAMIC50:  68   nM  BindingDB
EAMIC50:  78   nM  BindingDB
EAMIC50:  93   nM  BindingDB
EAMIC50:  98   nM  BindingDB
EAMKd:  50.5   nM  Binding MOAD
EAMIC50:  120   nM  BindingDB
EAMKd:  55.20000076293945   nM  BindingDB
EAMIC50:  145   nM  BindingDB
EAMIC50:  132   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.428α = 90
b = 44.333β = 90
c = 78.345γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-10-09 
  • Released Date: 2010-11-17 
  • Deposition Author(s): Chung, C.

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance