6FGF

Crystal Structure of BAZ2A bromodomain in complex with 1-methylpyridinone compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains.

Dalle Vedove, A.Spiliotopoulos, D.D'Agostino, V.G.Marchand, J.R.Unzue, A.Nevado, C.Lolli, G.Caflisch, A.

(2018) ChemMedChem 13: 1479-1487

  • DOI: 10.1002/cmdc.201800234
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bromodomain-containing protein BAZ2A is a validated target in prostate cancer, while the function of its paralog BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a very similar binding site for their natural ligand, the acetylat ...

    The bromodomain-containing protein BAZ2A is a validated target in prostate cancer, while the function of its paralog BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a very similar binding site for their natural ligand, the acetylated lysine side chain. Here, we present an analysis of the binding modes of eight compounds belonging to three distinct chemical classes. For all compounds, the moiety mimicking the natural ligand makes essentially identical interactions in the BAZ2A and BAZ2B bromodomains. In contrast, the rest of the molecule is partially solvent exposed and shows different orientations and interactions in the two bromodomains. Some of these differences could be exploited for designing selective inhibitors within the BAZ2 bromodomain subfamily.


    Organizational Affiliation

    Universita degli Studi di Trento, CIBIO, ITALY.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2A
A
105Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EN2
Query on EN2

Download SDF File 
Download CCD File 
A
~{N}-[3-[(4-fluorophenyl)carbonylamino]propyl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide
C17 H18 F N3 O3
UZLNHXVIIXNLFM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.801 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.339α = 90.00
b = 95.339β = 90.00
c = 32.546γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

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: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references