2ZJW

Crystal structure of human CK2 alpha complexed with Ellagic acid

• PDB DOI: https://doi.org/10.2210/pdb2ZJW/pdb

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


• Deposited: 2008-03-11 Released: 2009-03-17 
• Deposition Author(s): Sekiguchi, Y., Kinoshita, T., Nakaniwa, T., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Structural insight into human CK2alpha in complex with the potent inhibitor ellagic acid

Sekiguchi, Y., Nakaniwa, T., Kinoshita, T., Nakanishi, I., Kitaura, K., Hirasawa, A., Tsujimoto, G., Tada, T.

(2009) Bioorg Med Chem Lett 19: 2920-2923

• PubMed: 19414254 
• DOI: https://doi.org/10.1016/j.bmcl.2009.04.076
• Primary Citation of Related Structures:  
  2ZJW


• PubMed Abstract: 
  

  We determined the 2.35-A crystal structure of a human CK2 catalytic subunit (referred to as CK2alpha complexed with the ATP-competitive, potent CK2 inhibitor ellagic acid. The inhibitor binds to CK2alpha with a novel binding mode, including water-mediated hydrogen bonds. This structural information may support discovery of potent CK2 inhibitors.

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Organizational Affiliation: 

Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, 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: 40.78 kDa 
• Atom Count: 3,072 
• Modelled Residue Count: 332 
• 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  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
REF	B [auth A]	2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione C14 H6 O8 AFSDNFLWKVMVRB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
REF	PDBBind:  2ZJW	Ki: 20 (nM) from 1 assay(s)
	BindingDB:  2ZJW	Ki: 20 (nM) from 1 assay(s)
		IC50: 40 (nM) from 1 assay(s)
	Binding MOAD:  2ZJW	Ki: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.274 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.953	α = 90
b = 75.883	β = 90
c = 78.421	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Sekiguchi, Y., Kinoshita, T., Nakaniwa, T., Tada, T.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description