4FBX

Complex structure of human protein kinase CK2 catalytic subunit crystallized in the presence of a bisubstrate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A subnanomolar fluorescent probe for protein kinase CK2 interaction studies.

Enkvist, E.Viht, K.Bischoff, N.Vahter, J.Saaver, S.Raidaru, G.Issinger, O.G.Niefind, K.Uri, A.

(2012) Org.Biomol.Chem. 10: 8645-8653

  • DOI: 10.1039/c2ob26022k

  • PubMed Abstract: 
  • Up-regulation of an acidophilic protein kinase, CK2, has been established in several types of cancer. This cognition has made CK2 an important target for drug development for cancer chemotherapy. The characterization of potential drug candidates, det ...

    Up-regulation of an acidophilic protein kinase, CK2, has been established in several types of cancer. This cognition has made CK2 an important target for drug development for cancer chemotherapy. The characterization of potential drug candidates, determination of the structure and clarification of the functions of CK2 could be facilitated by the application of small-molecule fluorescent probes that bind to the active site of the enzyme with high affinity and selectivity. We have used a bisubstrate approach for the development of a highly potent inhibitor of CK2. 4,5,6,7-Tetrabromo-1H-benzimidazole was conjugated with peptides containing multiple aspartate residues via different linkers. The design of the inhibitors was by crystallographic analysis of the complex of an inhibitor with the catalytic subunit of the enzyme (CK2α). The inhibitory potency of the synthesized compounds was established in a kinetic assay that used thin layer chromatography for the measurement of the rate of phosphorylation of fluorescently labelled peptide 5-TAMRA-RADDSDDDDD. The most potent inhibitor, ARC-1502 (K(i) = 0.5 nM), revealed high selectivity for CK2α in a panel of 140 protein kinases. Labelling of ARC-1502 with PromoFluor-647 gave the fluorescent probe ARC-1504 that possessed subnanomolar affinity towards both CK2α and the holoenzyme. The probe was used in a fluorescence anisotropy-based binding assay to measure the concentration of CK2α and characterize non-labelled ligands binding to the active site of CK2α.


    Related Citations: 
    • Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
      Ermakova, I.,Boldyreff, B.,Issinger, O.G.,Niefind, K.
      (2003) J.Mol.Biol. 330: 925
    • Protein kinase CK2 in health and disease: Protein kinase CK2: from structures to insights.
      Niefind, K.,Raaf, J.,Issinger, O.G.
      (2009) Cell.Mol.Life Sci. 66: 1800
    • The catalytic subunit of human protein kinase CK2 structurally deviates from its maize homologue in complex with the nucleotide competitive inhibitor emodin.
      Raaf, J.,Klopffleisch, K.,Issinger, O.G.,Niefind, K.
      (2008) J.Mol.Biol. 377: 1


    Organizational Affiliation

    Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
bisubstrate inhibitor
B
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000870
Query on PRD_000870
Bbisubstrate inhibitorPolypeptide / Enzyme inhibitor

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0TJKi: 1450 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.114α = 90.00
b = 72.114β = 90.00
c = 135.056γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Other