2OXD | pdb_00002oxd

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

• PDB DOI: https://doi.org/10.2210/pdb2OXD/pdb

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


• Deposited: 2007-02-20 Released: 2007-09-25 
• Deposition Author(s): Battistutta, R., Zanotti, G., Cendron, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.273 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

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

• PubMed: 17768728 
• DOI: https://doi.org/10.1002/cbic.200700307
• Primary Citation Related Structures: 
  2OXD, 2OXX, 2OXY


• 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 0.15 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.74 kDa 
• Atom Count: 2,806 
• Modeled Residue Count: 325 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	332	Zea mays	Mutation(s): 0  Gene Names: ACK2 EC: 2.7.11.1
UniProt
Find proteins for P28523 (Zea mays) Explore P28523  Go to UniProtKB:  P28523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K32	B [auth A]	4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE C7 H2 Br4 N2 O BMVNFJCUHHTZQU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.273 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.148	α = 90
b = 60.316	β = 103.56
c = 46.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Battistutta, R., Zanotti, G., Cendron, L.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description