4IR4 | pdb_00004ir4

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)

• PDB DOI: https://doi.org/10.2210/pdb4IR4/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-14 Released: 2013-01-23 
• Deposition Author(s): Chaikuad, A., Felletar, I., Chung, C.W., Drewry, D., Chen, P., Filippakopoulos, P., Fedorov, O., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.228 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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

• PubMed: 25799074 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b00209
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemical Biology, GlaxoSmithKline , Research Triangle Park, 5 Moore Drive, Research Triangle Park, North Carolina 27709-3398, United States.
Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford OX3 7DQ, United Kingdom.
Computational & Structural Chemistry, Molecular Discovery Research, and ⊥Epinova, Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, United Kingdom.
Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, 69117 Heidelberg, Germany.
Nuffield Department of Clinical Medicine, Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ, United Kingdom.
Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University , Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.44 kDa 
• Atom Count: 1,162 
• Modeled Residue Count: 116 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2B	A	117	Homo sapiens	Mutation(s): 0  Gene Names: BAZ2B, KIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens) Explore Q9UIF8  Go to UniProtKB:  Q9UIF8
PHAROS:  Q9UIF8 GTEx:  ENSG00000123636

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IR4	B [auth A]	1-[7-(morpholin-4-yl)-1-(pyridin-2-yl)indolizin-3-yl]ethanone C19 H19 N3 O2 JNCJVBDKESBLNW-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.228 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.699	α = 90
b = 96.465	β = 90
c = 57.741	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Chaikuad, A., Felletar, I., Chung, C.W., Drewry, D., Chen, P., Filippakopoulos, P., Fedorov, O., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• 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