2YDW

Crystal Structure of the First Bromodomain of Human Brd2 with the inhibitor GW841819X


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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:  
    2YDW, 2YEK, 2YEL, 2YEM

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BROMODOMAIN-CONTAINING PROTEIN 2ABC153Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
NIH Common Fund Data Resources
PHAROS  P25440
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WSH
Query on WSH

Download CCD File 
A, B, C
BENZYL [(4R)-1-METHYL-6-PHENYL-4H-[1,2,4]TRIAZOLO[4,3-A][1,4]BENZODIAZEPIN-4-YL]CARBAMATE
C25 H21 N5 O2
TUWDLUFFAHHNEF-QHCPKHFHSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WSHIC50:  29.899999618530273   nM  Binding MOAD
WSHKd :  46   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.372α = 90
b = 56.013β = 93.98
c = 67.425γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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