6FGG

Crystal Structure of BAZ2A bromodomain in complex with 1-methylpyridinone compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 

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This is version 1.2 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: 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

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain adjacent to zinc finger domain protein 2A106Homo sapiensMutation(s): 0 
Gene Names: BAZ2AKIAA0314TIP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF9 (Homo sapiens)
Explore Q9UIF9 
Go to UniProtKB:  Q9UIF9
PHAROS:  Q9UIF9
GTEx:  ENSG00000076108 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIF9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D9B
Query on D9B

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-[2-(dimethylamino)ethyl]-2-oxidanylidene-1,3-benzoxazol-5-yl]-1-methyl-6-oxidanylidene-pyridine-3-carboxamide
C18 H20 N4 O4
RMQWPQCQFPMELT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
D9B Binding MOAD:  6FGG Kd: 1.70e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.408α = 90
b = 62.566β = 90
c = 69.387γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description