4XUB

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 bromodo ...

    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.


    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
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
43D
Query on 43D

Download CCD File 
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
 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 %)
43DIC50:  1070   nM  BindingDB
43DIC50:  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 = 81.17α = 90
b = 96.69β = 90
c = 57.81γ = 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: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references