2QC6

Protein kinase CK2 in complex with DBC

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Coumarin as attractive casein kinase 2 (CK2) inhibitor scaffold: an integrate approach to elucidate the putative binding motif and explain structure-activity relationships.

Chilin, A., Battistutta, R., Bortolato, A., Cozza, G., Zanatta, S., Poletto, G., Mazzorana, M., Zagotto, G., Uriarte, E., Guiotto, A., Pinna, L.A., Meggio, F., Moro, S.

(2008) J.Med.Chem. 51: 752-759

  • DOI: 10.1021/jm070909t

  • PubMed Abstract: 

    • Casein kinase 2 (CK2) is an ubiquitous, essential, and highly pleiotropic protein kinase whose abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other diseases. Recently, using different virtual ...

    Casein kinase 2 (CK2) is an ubiquitous, essential, and highly pleiotropic protein kinase whose abnormally high constitutive activity is suspected to underlie its pathogenic potential in neoplasia and other diseases. Recently, using different virtual screening approaches, we have identified several novel CK2 inhibitors. In particular, we have discovered that coumarin moiety can be considered an attractive CK2 inhibitor scaffold. In the present work, we have synthetized and tested a small library of coumarins (more than 60), rationalizing the observed structure-activity relationship. Moreover, the most promising inhibitor, 3,8-dibromo-7-hydroxy-4-methylchromen-2-one (DBC), has been also crystallized in complex with CK2, and the experimental binding mode has been used to derive a linear interaction energy (LIE) model.

    Organizational Affiliation: 

    Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, Padova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
332Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G12
Query on G12
Download SDF File 
Download CCD File 
A
3,8-DIBROMO-7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE
3,8-DIBROMO-7-HYDROXY-4-METHYLCHROMEN-2-ONE
C10 H6 Br2 O3
MSOLROYRAHCJNK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G12IC50: 100 nM BINDINGMOAD
DBCIC50: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.676α = 90.00
b = 60.252β = 103.00
c = 44.901γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-06-19 
  • Released Date: 2008-02-26 
  • Deposition Author(s): Battistutta, R.

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance