2YEK

Crystal Structure of the First Bromodomain of Human Brd2 with the inhibitor GSK525762 (IBET)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Characterization of Small Molecule Inhibitors of the Bet Family Bromodomains.

Chung, C.W.Coste, H.White, J.H.Mirguet, O.Wilde, J.Gosmini, R.L.Delves, C.Magny, S.M.Woodward, R.Hughes, S.A.Boursier, E.V.Flynn, H.Bouillot, A.M.Bamborough, P.Brusq, J.M.Gellibert, F.J.Jones, E.J.Riou, A.M.Homes, P.Martin, S.L.Uings, I.J.Toum, J.Clement, C.A.Boullay, A.B.Grimley, R.L.Blandel, F.M.Prinjha, R.K.Lee, K.Kirilovsky, J.Nicodeme, E.

(2011) J.Med.Chem. 54: 3827

  • DOI: 10.1021/jm200108t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Epigenetic mechanisms of gene regulation have a profound role in normal development and disease processes. An integral part of this mechanism occurs through lysine acetylation of histone tails which are recognized by bromodomains. While the biologica ...

    Epigenetic mechanisms of gene regulation have a profound role in normal development and disease processes. An integral part of this mechanism occurs through lysine acetylation of histone tails which are recognized by bromodomains. While the biological and structural characterization of many bromodomain containing proteins has advanced considerably, the therapeutic tractability of this protein family is only now becoming understood. This paper describes the discovery and molecular characterization of potent (nM) small molecule inhibitors that disrupt the function of the BET family of bromodomains (Brd2, Brd3, and Brd4). By using a combination of phenotypic screening, chemoproteomics, and biophysical studies, we have discovered that the protein-protein interactions between bromodomains and acetylated histones can be antagonized by selective small molecules that bind at the acetylated lysine recognition pocket. X-ray crystal structures of compounds bound into bromodomains of Brd2 and Brd4 elucidate the molecular interactions of binding and explain the precisely defined stereochemistry required for activity.


    Organizational Affiliation

    Molecular Discovery Research, GlaxoSmithKline R&D, Stevenage SG5 4HT, UK. Chun-Wa.H.Chung@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BROMODOMAIN-CONTAINING PROTEIN 2
A, B, C
153Homo sapiensMutation(s): 0 
Gene Names: BRD2 (KIAA9001, RING3)
Find proteins for P25440 (Homo sapiens)
Go to Gene View: BRD2
Go to UniProtKB:  P25440
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EAM
Query on EAM

Download SDF File 
Download CCD File 
A, B, C
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.243α = 90.00
b = 55.639β = 93.63
c = 66.231γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-03-25 
  • Released Date: 2011-06-15 
  • Deposition Author(s): Chung, C.W.

Revision History 

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Database references, Version format compliance