Human protein kinase CK2 alpha in complex with curcumin degradation products

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

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Biochemical and cellular mechanism of protein kinase CK2 inhibition by deceptive curcumin.

Cozza, G.Zonta, F.Dalle Vedove, A.Venerando, A.Dall'Acqua, S.Battistutta, R.Ruzzene, M.Lolli, G.

(2020) FEBS J 287: 1850-1864

  • DOI: https://doi.org/10.1111/febs.15111
  • Primary Citation of Related Structures:  
    6HOP, 6HOQ, 6HOR, 6HOT, 6HOU, 6HOV

  • PubMed Abstract: 

    Protein kinase CK2 is an antiapoptotic cancer-sustaining protein. Curcumin, reported previously as a CK2 inhibitor, is too bulky to be accommodated in the CK2 active site and rapidly degrades in solution generating various ATP-mimetic inhibitors; with a detailed comparative analysis, by means of both protein crystallography and enzymatic inhibition, ferulic acid was identified as the principal curcumin degradation product responsible for CK2 inhibition. The other curcumin derivatives vanillin, feruloylmethane and coniferyl aldehyde are weaker CK2 inhibitors. The high instability of curcumin in standard buffered solutions flags this compound, which is included in many commercial libraries, as a possible source of misleading interpretations, as was the case for CK2. Ferulic acid does not show any cytotoxicity and any inhibition of cellular CK2, due to its poor cellular permeability. However, curcumin acts as a prodrug in the cellular context, by generating its degradation products inside the treated cells, thus rescuing CK2 inhibition and consequently inducing cell death. Through the intracellular release of its degradation products, curcumin is expected to affect various target families; here, we identify the first bromodomain of BRD4 as a new target for those compounds. DATABASE: Structural data are available in the PDB database under the accession numbers 6HOP (CK2α/curcumin), 6HOQ (CK2α/ferulic acid), 6HOR (CK2α/feruloylmethane), 6HOT (CK2α/ferulic aldehyde), 6HOU (CK2α/vanillin) and 6HOV (BRD4/ferulic acid).

  • Organizational Affiliation

    Department of Molecular Medicine, University of Padua, Padua, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha336Homo sapiensMutation(s): 0 
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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FER

Download Ideal Coordinates CCD File 
C10 H10 O4
Query on GJK

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H [auth A](~{E})-4-(3-methoxy-4-oxidanyl-phenyl)but-3-en-2-one
C11 H12 O3
Query on CIY

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I [auth A](2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal
C10 H10 O3
Query on V55

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G [auth A]4-hydroxy-3-methoxybenzaldehyde
C8 H8 O3
Query on SO4

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B [auth A],
C [auth A],
D [auth A]
O4 S
Query on EDO

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E [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.158α = 90
b = 46.303β = 111.9
c = 63.344γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata 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: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2020-05-13
    Changes: Database references, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description