Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39935.93 
• Atom Count: 2748 
• Residue Count: 332 
• Unique protein chains: 1

1ZOH

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

• DOI: 10.2210/pdb1ZOH/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli


• Deposited: 2005-05-13 Released: 2005-11-29 
• Deposition Author(s): Battistutta, R., Mazzorana, M., Sarno, S., Kazimierczuk, Z., Zanotti, G., Pinna, L.A.

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Experimental Data Snapshot

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

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

• PubMed: 16298300 
• DOI: 10.1016/j.chembiol.2005.08.015
• Primary Citation of Related Structures:  
  1ZOG, 1ZOE
• Also Cited By: 3KXM, 3KXJ, 3KXG


• 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.

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Organizational Affiliation: 

Department of Chemistry, University of Padua, via Marzolo 1, 35131 Padua, Italy. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN KINASE CK2, ALPHA SUBUNIT	A	332	Zea mays	Mutation(s): 0  Gene Names: ACK2 EC: 2.7.11.1
Find proteins for P28523 (Zea mays) Go to UniProtKB:  P28523

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
K44	A	5,6,7,8-TETRABROMO-1-METHYL-2,3-DIHYDRO-1H-IMIDAZO[1,2-A]BENZIMIDAZOLE N1,N2-ETHYLENE-2-METHYLAMINO-4,5,6,7-TETRABROMO-BENZIMIDAZOLE C10 H7 Br4 N3 QHCZROILDUNGRT-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
K44	Ki: 100 nM BINDINGMOAD
K44	Ki: 100 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.221 
• R-Value Work: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 143.560	α = 90.00
b = 61.090	β = 102.70
c = 44.690	γ = 90.00

Software Package:

Software Name	Purpose
SHELX	model building
CCP4	data scaling
SHELXL-97	refinement
SHELX	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-13 
• Released Date: 2005-11-29 
• Deposition Author(s): Battistutta, R., Mazzorana, M., Sarno, S., Kazimierczuk, Z., Zanotti, G., Pinna, L.A.

Revision History 

• Version 1.0: 2005-11-29
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance