3KXG

Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor 3,4,5,6,7-pentabromo-1H-indazole (K64)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

ATP site-directed inhibitors of protein kinase CK2: an update.

Sarno, S.Papinutto, E.Franchin, C.Bain, J.Elliott, M.Meggio, F.Kazimierczuk, Z.Orzeszko, A.Zanotti, G.Battistutta, R.Pinna, L.A.

(2011) Curr Top Med Chem 11: 1340-1351

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CK2 denotes a pleiotropic, constitutively active protein kinase whose abnormally high level in many cancer cells is held as an example of "non oncogene addiction". A wide spectrum of cell permeable, fairly specific ATP site-directed CK2 inhibitors ar ...

    CK2 denotes a pleiotropic, constitutively active protein kinase whose abnormally high level in many cancer cells is held as an example of "non oncogene addiction". A wide spectrum of cell permeable, fairly specific ATP site-directed CK2 inhibitors are currently available which are proving useful to dissect its biological functions and which share the property of inducing apoptosis of cancer cells with no comparable effect on their "normal" counterparts. One of these, CX-4945, has recently entered clinical trials for the treatment of advanced solid tumors, Castelman's disease and multiple myeloma. The solution of a wide range of 3D structures of inhibitors bound to the catalytic subunits of CK2 reveals that their efficacy substantially relies on hydrophobic interactions within a cavity which is smaller than in other protein kinases. Accordingly the potency of tetra-halogenated benzimidazoles increases upon replacement of chlorine by bromine and, even more, by iodine, and decreases if two unique bulky side chains on CK2 (Val66 and Ile174) are mutated to alanines. Many CK2 inhibitors have been tested on a panel of more than 60 kinases providing Promiscuity Scores useful to evaluate their selectivity, the lowest value (9.47), denoting highest selectivity, being displayed by quinalizarin. The observation that CK2 inhibitors with medium/high promiscuity scores share the ability to inhibit a group of protein kinases as effectively as CK2 discloses the possibility of using their scaffolds for the rational development of selective inhibitors of these kinases, with special reference to PIMs, DYRKs, HIPK2, PKD and ERK8.


    Related Citations: 
    • Inspecting the structure-activity relationship of protein kinase CK2 inhibitors derived from tetrabromo-benzimidazole.
      Battistutta, R.,Mazzorana, M.,Sarno, S.,Kazimierczuk, Z.,Zanotti, G.,Pinna, L.A.
      (2005) Chem.Biol. 12: 1211
    • The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules.
      Battistutta, R.,Mazzorana, M.,Cendron, L.,Bortolato, A.,Sarno, S.,Kazimierczuk, Z.,Zanotti, G.,Moro, S.,Pinna, L.A.
      (2007) Chembiochem 8: 1804


    Organizational Affiliation

    Department of Biological Chemistry and CNR Institute of Neurosciences, University of Padova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
327Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K6X
Query on K6X

Download SDF File 
Download CCD File 
A
3,4,5,6,7-pentabromo-1H-indazole
C7 H Br5 N2
WQPXVZWNOLUBMY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.467α = 90.00
b = 60.370β = 103.13
c = 45.514γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description