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 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2B
A
117Homo sapiensGene Names: BAZ2B (KIAA1476)
Find proteins for Q9UIF8 (Homo sapiens)
Go to Gene View: BAZ2B
Go to UniProtKB:  Q9UIF8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
43D
Query on 43D

Download SDF File 
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 SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
43DIC50: 1070 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.170α = 90.00
b = 96.690β = 90.00
c = 57.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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