Crystal structure of human BAZ2B PHD zinc finger in complex with Fr23

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.

Amato, A.Lucas, X.Bortoluzzi, A.Wright, D.Ciulli, A.

(2018) ACS Chem Biol 13: 915-921

  • DOI: https://doi.org/10.1021/acschembio.7b01093
  • Primary Citation of Related Structures:  
    6FAP, 6FHQ, 6FHU, 6FI0, 6FI1, 6FKP

  • PubMed Abstract: 

    Plant homeodomain (PHD) zinc fingers are histone reader domains that are often associated with human diseases. Despite this, they constitute a poorly targeted class of readers, suggesting low ligandability. Here, we describe a successful fragment-based campaign targeting PHD fingers from the proteins BAZ2A and BAZ2B as model systems. We validated a pool of in silico fragments both biophysically and structurally and solved the first crystal structures of PHD zinc fingers in complex with fragments bound to an anchoring pocket at the histone binding site. The best-validated hits were found to displace a histone H3 tail peptide in competition assays. This work identifies new chemical scaffolds that provide suitable starting points for future ligand optimization using structure-guided approaches. The demonstrated ligandability of the PHD reader domains could pave the way for the development of chemical probes to drug this family of epigenetic readers.

  • Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2B
A, B
58Homo sapiensMutation(s): 0 
Gene Names: BAZ2BKIAA1476
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF8 (Homo sapiens)
Explore Q9UIF8 
Go to UniProtKB:  Q9UIF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.779α = 90
b = 45.47β = 90
c = 64.829γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-02
    Changes: Data collection, Database references