6FI0

Crystal structure of BAZ2A PHD zinc finger in complex with Fr 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/acschembio.7b01093
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plant homeodomain (PHD) zinc fingers are histone reader domains that often associate with human diseases. Despite this, they constitute a poorly targeted class of readers, suggesting low ligandability. Here, we describe a successful fragment-based ca ...

    Plant homeodomain (PHD) zinc fingers are histone reader domains that often associate 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 targets.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2A
A, B, C, D
58Homo sapiensMutation(s): 0 
Gene Names: BAZ2A (KIAA0314, TIP5)
Find proteins for Q9UIF9 (Homo sapiens)
Go to Gene View: BAZ2A
Go to UniProtKB:  Q9UIF9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DEW
Query on DEW

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B, C
2-azanyl-1-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl)ethanone
C9 H12 N2 O S
NRRHFNCSXNXKHA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.095α = 90.00
b = 72.095β = 90.00
c = 99.198γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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