1M2Q

Crystal structure of 1,8-di-hydroxy-4-nitro-xanten-9-one/CK2 kinase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of protein kinase CK2 by anthraquinone-related compounds. A structural insight

De Moliner, E.Moro, S.Sarno, S.Zagotto, G.Zanotti, G.Pinna, L.A.Battistutta, R.

(2003) J.Biol.Chem. 278: 1831-1836

  • DOI: 10.1074/jbc.M209367200
  • Primary Citation of Related Structures:  1M2P, 1M2R

  • PubMed Abstract: 
  • Protein kinases play key roles in signal transduction and therefore are among the most attractive targets for drug design. The pharmacological aptitude of protein kinase inhibitors is highlighted by the observation that various diseases with special ...

    Protein kinases play key roles in signal transduction and therefore are among the most attractive targets for drug design. The pharmacological aptitude of protein kinase inhibitors is highlighted by the observation that various diseases with special reference to cancer are because of the abnormal expression/activity of individual kinases. The resolution of the three-dimensional structure of the target kinase in complex with inhibitors is often the starting point for the rational design of this kind of drugs, some of which are already in advanced clinical trial or even in clinical practice. Here we present and discuss three new crystal structures of ATP site-directed inhibitors in complex with "casein kinase-2" (CK2), a constitutively active protein kinase implicated in a variety of cellular functions and misfunctions. With the help of theoretical calculations, we disclose some key features underlying the inhibitory efficiency of anthraquinone derivatives, outlining three different binding modes into the active site. In particular, we show that a nitro group in a hydroxyanthraquinone scaffold decreases the inhibitory constants K(i) because of electron-withdrawing and resonance effects that enhance the polarization of hydroxylic substituents in paraposition.


    Organizational Affiliation

    Department of Organic Chemistry, University of Padova, Padova 35131, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II, alpha chain
A
327Zea maysGene 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
MNX
Query on MNX

Download SDF File 
Download CCD File 
A
1,8-DI-HYDROXY-4-NITRO-XANTHEN-9-ONE
C13 H7 N O6
ZOHCDJRFYXKEQW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MNXKi: 800 nM (100) BINDINGDB
MNXKi: 800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.040α = 90.00
b = 51.730β = 99.33
c = 44.700γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance