2OXD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alpha A332Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Explore P28523 
Go to UniProtKB:  P28523
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K32
Query on K32

Download Ideal Coordinates CCD File 
A
4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE
C7 H2 Br4 N2 O
BMVNFJCUHHTZQU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K32Ki :  150   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.148α = 90
b = 60.316β = 103.56
c = 46.238γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



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