1ZOH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.chembiol.2005.08.015
  • Structures With Same Primary Citation

  • 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 ...

    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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN KINASE CK2, ALPHA SUBUNIT
A
332Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K44
Query on K44

Download CCD File 
A
5,6,7,8-TETRABROMO-1-METHYL-2,3-DIHYDRO-1H-IMIDAZO[1,2-A]BENZIMIDAZOLE
C10 H7 Br4 N3
QHCZROILDUNGRT-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K44Ki :  100   nM  PDBBind
K44Ki:  100   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.56α = 90
b = 61.09β = 102.7
c = 44.69γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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