3AXW | pdb_00003axw

Crystal structure of human CK2alpha complexed with a potent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3AXW/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-18 Released: 2012-04-04 
• Deposition Author(s): Kinoshita, T., Nakanishi, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.295 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Literature

Structure-Based Design of Novel Potent Protein Kinase CK2 (CK2) Inhibitors with Phenyl-azole Scaffolds

Hou, Z., Nakanishi, I., Kinoshita, T., Takei, Y., Yasue, M., Misu, R., Suzuki, Y., Nakamura, S., Kure, T., Ohno, H., Murata, K., Kitaura, K., Hirasawa, A., Tsujimoto, G., Oishi, S., Fujii, N.

(2012) J Med Chem 55: 2899-2903

• PubMed: 22339433 
• DOI: https://doi.org/10.1021/jm2015167
• Primary Citation Related Structures: 
  3AXW


• PubMed Abstract: 
  

  Protein kinase CK2 (CK2) is a ubiquitous serine/threonine protein kinase for hundreds of endogenous substrates. CK2 has been considered to be involved in many diseases, including cancers. Herein we report the discovery of a novel ATP-competitive CK2 inhibitor. Virtual screening of a compound library led to the identification of a hit 2-phenyl-1,3,4-thiadiazole compound. Subsequent structural optimization resulted in the identification of a promising 4-(thiazol-5-yl)benzoic acid derivative.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.7 kDa 
• Atom Count: 2,914 
• Modeled Residue Count: 329 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	340	Homo sapiens	Mutation(s): 0  Gene Names: CK2A1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens) Explore P68400  Go to UniProtKB:  P68400
PHAROS:  P68400 GTEx:  ENSG00000101266

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TID	B [auth A]	4-(5-amino-1,3,4-thiadiazol-2-yl)benzoic acid C9 H7 N3 O2 S LQHNMNCRCCSJQW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.295 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.186	α = 90
b = 80.216	β = 90
c = 83.329	γ = 90

Software Package:

Software Name	Purpose
PF	data collection
MOLREP	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Kinoshita, T., Nakanishi, I.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations