Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 2

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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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: https://doi.org/10.1002/cmdc.201800234
  • Primary Citation of Related Structures:  
    6FG6, 6FGF, 6FGG, 6FGH, 6FGI, 6FGL, 6FGT, 6FGU, 6FGV, 6FGW, 6FH6, 6FH7

  • 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 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

    Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2B117Homo 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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EN2

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-[(4-fluorophenyl)carbonylamino]propyl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide
C17 H18 F N3 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.57α = 90
b = 96.393β = 90
c = 57.952γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
STARANISOdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_169007

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references