4RVR

Crystal Structure of the bromodomain of human BAZ2B in complex WITH GSK2801


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B.

Chen, P.Chaikuad, A.Bamborough, P.Bantscheff, M.Bountra, C.Chung, C.W.Fedorov, O.Grandi, P.Jung, D.Lesniak, R.Lindon, M.Muller, S.Philpott, M.Prinjha, R.Rogers, C.Selenski, C.Tallant, C.Werner, T.Willson, T.M.Knapp, S.Drewry, D.H.

(2016) J Med Chem 59: 1410-1424

  • DOI: 10.1021/acs.jmedchem.5b00209
  • Primary Citation of Related Structures:  
    4IR5, 4IR6, 4IR3, 4IR4, 4RVR

  • PubMed Abstract: 
  • Bromodomains are acetyl-lysine specific protein interaction domains that have recently emerged as a new target class for the development of inhibitors that modulate gene transcription. The two closely related bromodomain containing proteins BAZ2A and ...

    Bromodomains are acetyl-lysine specific protein interaction domains that have recently emerged as a new target class for the development of inhibitors that modulate gene transcription. The two closely related bromodomain containing proteins BAZ2A and BAZ2B constitute the central scaffolding protein of the nucleolar remodeling complex (NoRC) that regulates the expression of noncoding RNAs. However, BAZ2 bromodomains have low predicted druggability and so far no selective inhibitors have been published. Here we report the development of GSK2801, a potent, selective and cell active acetyl-lysine competitive inhibitor of BAZ2A and BAZ2B bromodomains as well as the inactive control compound GSK8573. GSK2801 binds to BAZ2 bromodomains with dissociation constants (KD) of 136 and 257 nM for BAZ2B and BAZ2A, respectively. Crystal structures demonstrated a canonical acetyl-lysine competitive binding mode. Cellular activity was demonstrated using fluorescent recovery after photobleaching (FRAP) monitoring displacement of GFP-BAZ2A from acetylated chromatin. A pharmacokinetic study in mice showed that GSK2801 had reasonable in vivo exposure after oral dosing, with modest clearance and reasonable plasma stability. Thus, GSK2801 represents a versatile tool compound for cellular and in vivo studies to understand the role of BAZ2 bromodomains in chromatin biology.


    Organizational Affiliation

    Department of Chemical Biology, GlaxoSmithKline , Research Triangle Park, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2BA117Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
NIH Common Fund Data Resources
PHAROS  Q9UIF8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3WQ
Query on 3WQ

Download CCD File 
A
1-{1-[2-(methylsulfonyl)phenyl]-7-propoxyindolizin-3-yl}ethanone
C20 H21 N O4 S
KHWCPNJRJCNVRI-UHFFFAOYSA-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 %)
3WQIC50:  360   nM  BindingDB
3WQKd:  136   nM  BindingDB
3WQIC50:  430   nM  BindingDB
3WQKd:  60   nM  BindingDB
3WQKd:  3162   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.72α = 90
b = 96.975β = 90
c = 58.06γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2015-09-02
    Changes: Database references
  • Version 1.4: 2016-03-16
    Changes: Database references