7ZWE

The Crystal structure of GW8695 bound to CK2alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors.

Reinecke, M.Brear, P.Vornholz, L.Berger, B.T.Seefried, F.Wilhelm, S.Samaras, P.Gyenis, L.Litchfield, D.W.Medard, G.Muller, S.Ruland, J.Hyvonen, M.Wilhelm, M.Kuster, B.

(2024) Nat Chem Biol 20: 577-585

  • DOI: https://doi.org/10.1038/s41589-023-01459-3
  • Primary Citation of Related Structures:  
    7A4Q, 7ZWE, 7ZWG

  • PubMed Abstract: 

    Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Compounds targeting PKN3 were discovered and phosphoproteomics identified substrates that indicate target engagement in cells. We anticipate that this molecular resource will aid research in drug discovery and chemical biology.


  • Organizational Affiliation

    Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha327Homo sapiensMutation(s): 4 
Gene Names: CSNK2A1CK2A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QXZ (Subject of Investigation/LOI)
Query on QXZ

Download Ideal Coordinates CCD File 
B [auth A]7-(1~{H}-indol-2-yl)-5-methyl-~{N}-(3,4,5-trimethoxyphenyl)imidazo[5,1-f][1,2,4]triazin-2-amine
C23 H22 N6 O3
LXDPQXXUVGVIND-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.01α = 90
b = 45.376β = 111.45
c = 63.508γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description
  • Version 1.3: 2024-05-15
    Changes: Database references