Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32

Experimental Data Snapshot

  • Resolution: 1.81 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

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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: 1804-1809

  • DOI: https://doi.org/10.1002/cbic.200700307
  • Primary Citation of Related Structures:  
    2OXD, 2OXX, 2OXY

  • PubMed Abstract: 

    CK2 is a highly pleiotropic Ser/Thr protein kinase that is able to promote cell survival and enhance the tumour phenotype under specific circumstances. We have determined the crystal structure of three new complexes with tetrabromobenzimidazole derivatives that display K(i) values between 0.15 and 0.30 microM. A comparative analysis of these data with those of four other inhibitors of the same family revealed the presence of some highly conserved water molecules in the ATP-binding site. These waters reside near Lys68, in an area with a positive electrostatic potential that is able to attract and orient negatively charged ligands. The presence of this positive region and two unique bulky residues that are typical of CK2, Ile66 and Ile174, play a critical role in determining the ligand orientation and binding selectivity.

  • Organizational Affiliation

    Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy. roberto. battistutta@unipd.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
332Zea maysMutation(s): 0 
Gene Names: ACK2
Find proteins for P28523 (Zea mays)
Explore P28523 
Go to UniProtKB:  P28523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on K17

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C7 H2 Br4 N2
Binding Affinity Annotations 
IDSourceBinding Affinity
K17 PDBBind:  2OXY Ki: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.81 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.287α = 91.9
b = 57.44β = 103.86
c = 62.467γ = 97.51
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description