Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.94 kDa 
• Atom Count: 3127 
• Modelled Residue Count: 326 
• Deposited Residue Count: 332 
• Unique protein chains: 1

1ZOH

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

• PDB DOI: 10.2210/pdb1ZOH/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• 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 
• R-Value Observed: 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:  
  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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN KINASE CK2, ALPHA SUBUNIT	A	332	Zea mays	Mutation(s): 0  Gene Names: ACK2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for P28523 (Zea mays) Explore P28523  Go to UniProtKB:  P28523

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
K44	Binding MOAD:  1ZOH	Ki: 100 (nM) from 1 assay(s)
	PDBBind:  1ZOH	Ki: 100 (nM) from 1 assay(s)

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 = 143.56	α = 90
b = 61.09	β = 102.7
c = 44.69	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance