Crystal structure of protein kinase CK2 in complex with TBB-derivatives

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

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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: 1211-1219

  • DOI: https://doi.org/10.1016/j.chembiol.2005.08.015
  • Primary Citation of Related Structures:  
    1ZOE, 1ZOG, 1ZOH

  • PubMed Abstract: 

    CK2 is a very pleiotropic protein kinase whose high constitutive activity is suspected to cooperate to neoplasia. Here, the crystal structure of the complexes between CK2 and three selective tetrabromo-benzimidazole derivatives inhibiting CK2 with Ki values between 40 and 400 nM are presented. The ligands bind to the CK2 active site in a different way with respect to the parent compound TBB. They enter more deeply into the cavity, establishing halogen bonds with the backbone of Glu114 and Val116 in the hinge region. A detailed analysis of the interactions highlights a major role of the hydrophobic effect in establishing the rank of potency within this class of inhibitors and shows that polar interactions are responsible for the different orientation of the molecules in the active site.

  • Organizational Affiliation

    Department of Chemistry, University of Padua, via Marzolo 1, 35131 Padua, Italy. roberto.battistutta@unipd.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN KINASE CK2, alpha SUBUNIT332Zea 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 K37

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C8 H4 Br4 N2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
K37 PDBBind:  1ZOG Ki: 70 (nM) from 1 assay(s)
Binding MOAD:  1ZOG Ki: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.05α = 90
b = 58.81β = 103.3
c = 45.75γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations