Crystal structure of CK2a1 H115Y with hematein

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.187 

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Structural insights for producing CK2 alpha 1-specific inhibitors.

Tsuyuguchi, M.Nakaniwa, T.Hirasawa, A.Nakanishi, I.Kinoshita, T.

(2020) Bioorg Med Chem Lett 30: 126837-126837

  • DOI: https://doi.org/10.1016/j.bmcl.2019.126837
  • Primary Citation of Related Structures:  
    6L1Z, 6L20, 6L21, 6L22, 6L23, 6L24

  • PubMed Abstract: 

    Casein kinase 2 catalytic subunit (CK2α) is classified into two subtypes CK2α1 and CK2α2. CK2α1 is a drug discovery target, whereas CK2α2 is an off-target of CK2α1 inhibitors. High amino acid sequence homology between these subtypes hampers efforts to produce ATP competitive inhibitors that are highly selective to CK2α1. Hematein was identified previously as a non-ATP-competitive inhibitor for CK2α1, whereas this compound acts as an ATP competitive CK2α2 inhibitor. Crystal structures of CK2α1 and CK2α2 in complex with hematein revealed distinct binding features that provide structural insights for producing CK2α1-selective inhibitors.

  • Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: tsuyuguchi13@b.s.osakafu-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha340Homo sapiensMutation(s): 1 
Gene Names: CSNK2A1CK2A1
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
E3U (Subject of Investigation/LOI)
Query on E3U

Download Ideal Coordinates CCD File 
B [auth A](6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one
C16 H12 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.107α = 90
b = 79.21β = 90
c = 82.657γ = 90
Software Package:
Software NamePurpose
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: 2020-02-26
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description