Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.95 kDa 
• Atom Count: 2909 
• Residue Count: 327 
• Unique protein chains: 1

1M2Q

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

• DOI: 10.2210/pdb1M2Q/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-06-25 Released: 2003-06-17 
• Deposition Author(s): De Moliner, E., Sarno, S., Moro, S., Zagotto, G., Zanotti, G., Pinna, L.A., Battistutta, R.

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Experimental Data Snapshot

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

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

• PubMed: 12419810 
• DOI: 10.1074/jbc.M209367200
• Primary Citation of Related Structures:  
  1M2R, 1M2Q, 1M2P


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II, alpha chain	A	327	Zea mays	Mutation(s): 0  Gene Names: ACK2 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for P28523 (Zea mays) Explore P28523  Go to UniProtKB:  P28523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNX	A	1,8-DI-HYDROXY-4-NITRO-XANTHEN-9-ONE C13 H7 N O6 ZOHCDJRFYXKEQW-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MNX	Ki:  800   nM  BindingDB
MNX	Ki :  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 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.04	α = 90
b = 51.73	β = 99.33
c = 44.7	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-25 
• Released Date: 2003-06-17 
Deposition Author(s): De Moliner, E., Sarno, S., Moro, S., Zagotto, G., Zanotti, G., Pinna, L.A., Battistutta, R.

Revision History 

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