6L20

Crystal structure of CK2a2 with hematein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.249 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alpha'A,
B [auth D],
C [auth G],
D [auth J]
338Homo sapiensMutation(s): 0 
Gene Names: CSNK2A2CK2A2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens)
Explore P19784 
Go to UniProtKB:  P19784
PHAROS:  P19784
GTEx:  ENSG00000070770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19784
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E3U (Subject of Investigation/LOI)
Query on E3U

Download Ideal Coordinates CCD File 
E [auth A],
G [auth D],
I [auth G],
J
(6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one
C16 H12 O6
HLUCICHZHWJHLL-INIZCTEOSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
H [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.249 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.7α = 81.154
b = 89.137β = 86.049
c = 95.994γ = 90.063
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release