Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 14.16 kDa 
• Atom Count: 1160 
• Residue Count: 116 
• Unique protein chains: 1

4XUB

Crystal Structure of the bromodomain of human BAZ2B in complex with BAZ2-ICR chemical probe

• DOI: 10.2210/pdb4XUB/pdb

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


• Deposited: 2015-01-25 Released: 2015-03-11 
• Deposition Author(s): Chaikuad, A., Felletar, I., 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: 1.98 Å
• R-Value Free: 0.215 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B.

Drouin, L., McGrath, S., Vidler, L.R., Chaikuad, A., Monteiro, O., Tallant, C., Philpott, M., Rogers, C., Fedorov, O., Liu, M., Akhtar, W., Hayes, A., Raynaud, F., Muller, S., Knapp, S., Hoelder, S.

(2015) J Med Chem 58: 2553-2559

• PubMed: 25719566 
• DOI: 10.1021/jm501963e
• Primary Citation of Related Structures:  
  4XUA, 4XUB


• PubMed Abstract: 
  

The bromodomain containing proteins BAZ2A/B play essential roles in chromatin remodeling and regulation of noncoding RNAs. We present the structure based discovery of a potent, selective, and cell active inhibitor 13 (BAZ2-ICR) of the BAZ2A/B bromodomains through rapid optimization of a weakly potent starting point. A key feature of the presented inhibitors is an intramolecular aromatic stacking interaction that efficiently occupies the shallow bromodomain pockets. 13 represents an excellent chemical probe for functional studies of the BAZ2 bromodomains in vitro and in vivo.

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Organizational Affiliation: 

The Institute of Cancer Research, Division of Cancer Therapeutics, Cancer Research UK Cancer Therapeutics Unit , 15 Cotswold Road, Sutton, London SM2 5NG, U.K.

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
Find proteins for Q9UIF8 (Homo sapiens) Explore Q9UIF8  Go to UniProtKB:  Q9UIF8
NIH Common Fund Data Resources
PHAROS  Q9UIF8 GTEx  ENSG00000123636

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
43D	A	4-{4-(1-methyl-1H-pyrazol-4-yl)-1-[2-(4-methyl-1H-1,2,3-triazol-1-yl)ethyl]-1H-imidazol-5-yl}benzonitrile C19 H18 N8 YPRKVQKJNRKXFN-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
43D	IC50:  1070   nM  BindingDB
43D	IC50:  1070   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.215 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.17	α = 90
b = 96.69	β = 90
c = 57.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-25 
• Released Date: 2015-03-11 
Deposition Author(s): Chaikuad, A., Felletar, I., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-03-25
  Changes: Database references