Crystal Structure of the bromodomain of human BAZ2B in complex with 1-[7-(morpholin-4-yl)-1-(pyridin-2-yl)indolizin-3-yl]ethanone (GSK2834113A)

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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

    Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2B117Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
GTEx:  ENSG00000123636 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IR4

Download Ideal Coordinates CCD File 
B [auth A]1-[7-(morpholin-4-yl)-1-(pyridin-2-yl)indolizin-3-yl]ethanone
C19 H19 N3 O2
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.699α = 90
b = 96.465β = 90
c = 57.741γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2015-09-09
    Changes: Database references
  • Version 1.4: 2015-10-21
    Changes: Database references
  • Version 1.5: 2016-04-20
    Changes: Database references
  • Version 1.6: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description