Crystal Structure of maize CK2 in complex with tyrphostin AG99

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

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Inhibition of protein kinase CK2 by flavonoids and tyrphostins. A structural insight.

Lolli, G.Cozza, G.Mazzorana, M.Tibaldi, E.Cesaro, L.Donella-Deana, A.Meggio, F.Venerando, A.Franchin, C.Sarno, S.Battistutta, R.Pinna, L.A.

(2012) Biochemistry 51: 6097-6107

  • DOI: https://doi.org/10.1021/bi300531c
  • Primary Citation of Related Structures:  
    4DGM, 4DGN, 6QS5

  • PubMed Abstract: 

    Sixteen flavonoids and related compounds have been tested for their ability to inhibit three acidophilic Ser/Thr protein kinases: the Golgi apparatus casein kinase (G-CK) recently identified with protein FAM20C, protein kinase CK1, and protein kinase CK2. While G-CK is entirely insensitive to all compounds up to 40 μM concentration, consistent with the view that it is not a member of the kinome, and CK1 is variably inhibited in an isoform-dependent manner by fisetin and luteolin, and to a lesser extent by myricetin and quercetin, CK2 is susceptible to drastic inhibition by many flavonoids, displaying with six of them IC(50) values < 1 μM. A common denominator of these compounds (myricetin, quercetin, fisetin, kaempferol, luteolin, and apigenin) is a flavone scaffold with at least two hydroxyl groups at positions 7 and 4'. Inhibition is competitive with respect to the phospho-donor substrate ATP. The crystal structure of apigenin and luteolin in complex with the catalytic subunit of Zea mays CK2 has been solved, revealing their ability to interact with both the hinge region (Val116) and the positive area near Lys68 and the conserved water W1, the two main polar ligand anchoring points in the CK2 active site. Modeling experiments account for the observation that luteolin but not apigenin inhibits also CK1. The observation that luteolin shares its pyrocatechol moiety with tyrphostin AG99 prompted us to solve also the structure of this compound in complex with CK2. AG99 was found inside the ATP pocket, consistent with its mode of inhibition competitive with respect to ATP. As in the case of luteolin, the pyrocatechol group of AG99 is critical for binding, interacting with the positive area in the deepest part of the CK2 active site.

  • Organizational Affiliation

    Venetian Institute of Molecular Medicine (VIMM), Padova, Italy, Via G. Orus 2 35129 Padova, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha325Zea maysMutation(s): 0 
Gene Names: ACK2
Find proteins for P28523 (Zea mays)
Explore P28523 
Go to UniProtKB:  P28523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JGB

Download Ideal Coordinates CCD File 
B [auth A](~{E})-3-[3,4-bis(oxidanyl)phenyl]-2-cyano-prop-2-enamide
C10 H8 N2 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.97α = 90
b = 59.55β = 103.81
c = 46.35γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description