5M56

Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2alpha') with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 2.0 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 (Basel) 10

  • DOI: 10.3390/ph10010009
  • Primary Citation of Related Structures:  
    5M44, 5M4C, 5M4F, 5M4I, 5M4U, 5M56

  • 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 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 ...

    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: 

    Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo Street, 03680 Kyiv, Ukraine. yarmolyuksm@gmail.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alpha'A, B364Homo sapiensMutation(s): 2 
Gene Names: CSNK2A2, CK2A2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens)
Explore P19784 
Go to UniProtKB:  P19784
PHAROS:  P19784
GTEx:  ENSG00000070770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19784
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7FC
Query on 7FC
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid
C16 H8 Cl2 O5
CFWCAEJMOUILDR-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B],
I [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.341α = 90
b = 87.62β = 109.69
c = 72.977γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyNI 643/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-05-10
    Changes: Database references
  • Version 1.3: 2017-05-17
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.0: 2018-10-10
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary