6FGU

Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 

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 research, whereas the function of its paralogue BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a similar binding site for their natural ligand, the ...

    The bromodomain-containing protein BAZ2A is a validated target in prostate cancer research, whereas the function of its paralogue BAZ2B is still undefined. The bromodomains of BAZ2A and BAZ2B have a 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 engages in essentially identical interactions in the BAZ2A and BAZ2B bromodomains. In contrast, the rest of the molecule is partially solvent-exposed and adopts different orientations with different interactions in the two bromodomains. Some of these differences could be exploited for designing inhibitors with selectivity within the BAZ2 bromodomain subfamily.


    Organizational Affiliation

    Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123, Povo-Trento, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bromodomain adjacent to zinc finger domain protein 2B
A
117Homo 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
D9Q
Query on D9Q

Download SDF File 
Download CCD File 
A
1-methyl-6-oxidanylidene-~{N}-(2-pyrrolidin-1-ylethyl)pyridine-3-carboxamide
C13 H19 N3 O2
BHVHUAARAHRDNS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.626α = 90.00
b = 96.163β = 90.00
c = 57.846γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

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