Crystal structure of human CK2 alpha complexed with Ellagic acid

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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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

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

  • 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.

  • Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha340Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on REF

Download Ideal Coordinates CCD File 
B [auth A]2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione
C14 H6 O8
Binding Affinity Annotations 
IDSourceBinding 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

  • 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 = 47.953α = 90
b = 75.883β = 90
c = 78.421γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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