5M4F

Complex structure of human protein kinase CK2 catalytic subunit with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) crystallized under low-salt conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.519 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor.

Niefind, K.Bischoff, N.Golub, A.G.Bdzhola, V.G.Balanda, A.O.Prykhod'ko, A.O.Yarmoluk, S.M.

(2017) Pharmaceuticals 10: --

  • DOI: 10.3390/ph10010009
  • Primary Citation of Related Structures:  
  • Also Cited By: 5N9N, 5N9L, 5N9K

  • PubMed Abstract: 
  • Protein kinase CK2 is associated with a number of human diseases, among them cancer, and is therefore a target for inhibitor development in industry and academia. Six crystal structures of either CK2α, the catalytic subunit of human protein kinase CK ...

    Protein kinase CK2 is associated with a number of human diseases, among them cancer, and is therefore a target for inhibitor development in industry and academia. Six crystal structures of either CK2α, the catalytic subunit of human protein kinase CK2, or its paralog CK2α' in complex with two ATP-competitive inhibitors-based on either a flavonol or a thieno[2,3-d]pyrimidine framework-are presented. The structures show examples for extreme structural deformations of the ATP-binding loop and its neighbourhood and of the hinge/helix αD region, i.e., of two zones of the broader ATP site environment. Thus, they supplement our picture of the conformational space available for CK2α and CK2α'. Further, they document the potential of synthetic ligands to trap unusual conformations of the enzymes and allow to envision a new generation of inhibitors that stabilize such conformations.


    Related Citations: 
    • A Note of Caution on the Role of Halogen Bonds for Protein Kinase/Inhibitor Recognition Suggested by High- And Low-Salt CK2alpha Complex Structures.
      Guerra, B.,Bischoff, N.,Bdzhola, V.G.,Yarmoluk, S.M.,Issinger, O.G.,Golub, A.G.,Niefind, K.
      (2015) ACS Chem. Biol. 10: 1654
    • Synthesis and biological evaluation of substituted (thieno[2,3-d]pyrimidin-4-ylthio)carboxylic acids as inhibitors of human protein kinase CK2.
      Golub, A.G.,Bdzhola, V.G.,Briukhovetska, N.V.,Balanda, A.O.,Kukharenko, O.P.,Kotey, I.M.,Ostrynska, O.V.,Yarmoluk, S.M.
      (2011) Eur J Med Chem 46: 870
    • Structure-based discovery of novel flavonol inhibitors of human protein kinase CK2.
      Golub, A.G.,Bdzhola, V.G.,Kyshenia, Y.V.,Sapelkin, V.M.,Prykhod'ko, A.O.,Kukharenko, O.P.,Ostrynska, O.V.,Yarmoluk, S.M.
      (2011) Mol. Cell. Biochem. 356: 107


    Organizational Affiliation

    Department für Chemie, Institut für Biochemie, Universität zu Köln, Otto-Fischer-Straße 12-14, D-50674 Köln, Germany. Karsten.Niefind@uni-koeln.de.




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
Small Molecules
Ligands 3 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
7FC
Query on 7FC

Download SDF File 
Download CCD File 
A
4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid
C16 H8 Cl2 O5
CFWCAEJMOUILDR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.519 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.033α = 90.00
b = 79.569β = 90.00
c = 82.142γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyNI 643/4-2

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-05-10
    Type: Database references
  • Version 1.3: 2017-05-17
    Type: Database references
  • Version 1.4: 2017-09-06
    Type: Author supporting evidence