4RLK

Crystal structure of Z. mays CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Protein kinase CK2 inhibition is associated with the destabilization of HIF-1 alpha in human cancer cells.

Guerra, B.Rasmussen, T.D.Schnitzler, A.Jensen, H.H.Boldyreff, B.S.Miyata, Y.Marcussen, N.Niefind, K.Issinger, O.G.

(2015) Cancer Lett 356: 751-761

  • DOI: 10.1016/j.canlet.2014.10.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Screening for protein kinase CK2 inhibitors of the structural diversity compound library (DTP NCI/NIH) led to the discovery of 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl]benzoic acid (E9). E9 induces apoptotic cell death in various cancer cell ...

    Screening for protein kinase CK2 inhibitors of the structural diversity compound library (DTP NCI/NIH) led to the discovery of 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl]benzoic acid (E9). E9 induces apoptotic cell death in various cancer cell lines and upon hypoxia, the compound suppresses CK2-catalyzed HSP90/Cdc37 phosphorylation and induces HIF-1α degradation. Furthermore, E9 exerts a strong anti-tumour activity by inducing necrosis in murine xenograft models underlining its potential to be used for cancer treatment in future clinical studies. Crystal structure analysis of human and maize CK2α in complex with E9 reveals unique binding properties of the inhibitor to the enzyme, accounting for its affinity and selectivity.


    Organizational Affiliation

    KinaseDetect Aps, Odense, Denmark.,Institute of Pathology, OUH, Odense, Denmark.,Department of Cell & Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Biomedical Research Group, BMB, University of Southern Denmark, Odense, Denmark; KinaseDetect Aps, Odense, Denmark. Electronic address: ogi@bmb.sdu.dk.,Department of Chemistry, Institute of Biochemistry, University of Cologne, Cologne, Germany.,Biomedical Research Group, BMB, University of Southern Denmark, Odense, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
332Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
E91
Query on E91

Download SDF File 
Download CCD File 
A
4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid
C21 H14 N2 O2
UDYNXPSETJWNEU-LPYMAVHISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.748α = 90.00
b = 59.683β = 102.96
c = 44.884γ = 90.00
Software Package:
Software NamePurpose
CORRECTdata scaling
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release