5MGG

Crystal Structure of BAZ2B bromodomain in complex with 4-chloropyridine derivative 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of BAZ2A bromodomain ligands.

Spiliotopoulos, D.Wamhoff, E.C.Lolli, G.Rademacher, C.Caflisch, A.

(2017) Eur J Med Chem 139: 564-572

  • DOI: 10.1016/j.ejmech.2017.08.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) is implicated in aggressive prostate cancer. The BAZ2A bromodomain is a challenging target because of the shallow pocket of its natural ligand, the acetylated side chain of lysine. Her ...

    The bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) is implicated in aggressive prostate cancer. The BAZ2A bromodomain is a challenging target because of the shallow pocket of its natural ligand, the acetylated side chain of lysine. Here, we report the successful screening of a library of nearly 1500 small molecules by high-throughput docking and force field-based binding-energy evaluation. For seven of the 20 molecules selected in silico, evidence of binding to the BAZ2A bromodomain is provided by ligand-observed NMR spectroscopy. Two of these compounds show a favorable ligand efficiency of 0.42 kcal/mol per non-hydrogen atom in a competition-binding assay. The crystal structures of the BAZ2A bromodomain in complex with four fragment hits validate the predicted binding modes. The binding modes of compounds 1 and 3 are compatible with ligand growing for optimization of affinity for BAZ2A and selectivity against the close homologue BAZ2B.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2B
A
116Homo sapiensMutation(s): 0 
Gene Names: BAZ2B (KIAA1476)
Find proteins for Q9UIF8 (Homo sapiens)
Go to Gene View: BAZ2B
Go to UniProtKB:  Q9UIF8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MU
Query on 7MU

Download SDF File 
Download CCD File 
A
4-chloranyl-~{N}-methyl-pyridine-2-carboxamide
C7 H7 Cl N2 O
BGVBBMZMEKXUTR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 80.702α = 90.00
b = 96.706β = 90.00
c = 57.547γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_169007

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Database references, Refinement description