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 
  • R-Value Observed: 0.189 

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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:  
    3NGA, 3NSZ

  • 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 pathways that regulate transcription, and has been implicated in cancer ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alphaA, B333Homo sapiensMutation(s): 0 
Gene Names: CK2, CK2A1, CSNK2A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3NG
Query on 3NG
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]		5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C19 H12 Cl N3 O2
MUOKSQABCJCOPU-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3NG BindingDB:  3NGA Ki: min: 0.22, max: 0.38 (nM) from 2 assay(s)
Kd: min: 0.56, max: 0.56 (nM) from 2 assay(s)
IC50: min: 0.3, max: 2000 (nM) from 17 assay(s)
PDBBind:  3NGA Kd: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.64α = 90
b = 127.64β = 90
c = 125.75γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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