3NGA

Human CK2 catalytic domain in complex with CX-4945

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


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

Literature

Structural basis of CX-4945 binding to human protein kinase CK2.

Ferguson, A.D., Sheth, P.R., Basso, A.D., Paliwal, S., Gray, K., Fischmann, T.O., Le, H.V.

(2011) Febs Lett. 585: 104-110

  • DOI: 10.1016/j.febslet.2010.11.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Protein kinase CK2 (CK2), a constitutively active serine/threonine kinase, is involved in a variety of roles essential to the maintenance of cellular homeostasis. Elevated levels of CK2 expression results in the dysregulation of key signaling pathway ...

    Protein kinase CK2 (CK2), a constitutively active serine/threonine kinase, is involved in a variety of roles essential to the maintenance of cellular homeostasis. Elevated levels of CK2 expression results in the dysregulation of key signaling pathways that regulate transcription, and has been implicated in cancer. The adenosine-5'-triphosphate-competitive inhibitor CX-4945 has been reported to show broad spectrum anti-proliferative activity in multiple cancer cell lines. Although the enzymatic IC(50) of CX-4945 has been reported, the thermodynamics and structural basis of binding to CK2α remained elusive. Presented here are the crystal structures of human CK2α in complex with CX-4945 and adenylyl phosphoramidate at 2.7 and 1.3 Å, respectively. Biophysical analysis of CX-4945 binding is also described. This data provides the structural rationale for the design of more potent inhibitors against this emerging cancer target.

    Organizational Affiliation: 

    Drug Design Department, Merck Research Laboratory, Kenilworth, NJ 07033, USA. andrew.ferguson@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A, B
333Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3NG
Query on 3NG
Download SDF File 
Download CCD File 
A, B
5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C19 H12 Cl N3 O2
MUOKSQABCJCOPU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3NGIC50: 11 nM (85) BINDINGDB
3NGKd: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 127.640α = 90.00
b = 127.640β = 90.00
c = 125.750γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
XDSdata reduction
BUSTERrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2010-06-11 
  • Released Date: 2010-12-15 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance