3R0T

Crystal structure of human protein kinase CK2 alpha subunit in complex with the inhibitor CX-5279


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer.

Battistutta, R.Cozza, G.Pierre, F.Papinutto, E.Lolli, G.Sarno, S.O'Brien, S.E.Siddiqui-Jain, A.Haddach, M.Anderes, K.Ryckman, D.M.Meggio, F.Pinna, L.A.

(2011) Biochemistry 50: 8478-8488

  • DOI: 10.1021/bi2008382
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 5-(3-Chlorophenylamino)benzo[c][2,6]naphthyridine-8-carboxylic acid (CX-4945), the first clinical stage inhibitor of protein kinase CK2 for the treatment of cancer, is representative of a new class of CK2 inhibitors with K(i) values in the low nanomo ...

    5-(3-Chlorophenylamino)benzo[c][2,6]naphthyridine-8-carboxylic acid (CX-4945), the first clinical stage inhibitor of protein kinase CK2 for the treatment of cancer, is representative of a new class of CK2 inhibitors with K(i) values in the low nanomolar range and unprecedented selectivity versus other kinases. Here we present the crystal structure of the complexes of CX-4945 and two analogues (CX-5011 and CX-5279) with the catalytic subunit of human CK2. Consistent with their ATP-competitive mode of inhibition, all three compounds bind in the active site of CK2 (type I inhibitors). The tricyclic scaffold of the inhibitors superposes on the adenine of ATP, establishing multiple hydrophobic interactions with the binding cavity. The more extended scaffold, as compared to that of ATP, allows the carboxylic function, shared by all three ligands, to penetrate into the deepest part of the active site where it makes interactions with conserved water W1 and Lys-68, thus accounting for the crucial role of this negatively charged group in conferring high potency to this class of inhibitors. The presence of a pyrimidine in CX-5011 and in CX-5279 instead of a pyridine (as in CX-4945) ring is likely to account for the higher specificity of these compounds whose Gini coefficients, calculated by profiling them against panels of 102 and/or 235 kinases, are significantly higher than that of CX-4945 (0.735 and 0.755, respectively, vs 0.615), marking the highest selectivity ever reported for CK2 inhibitors.


    Related Citations: 
    • Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2.
      Cozza, G.,Mazzorana, M.,Papinutto, E.,Bain, J.,Elliott, M.,di Maira, G.,Gianoncelli, A.,Pagano, M.A.,Sarno, S.,Ruzzene, M.,Battistutta, R.,Meggio, F.,Moro, S.,Zagotto, G.,Pinna, L.A.
      (2009) Biochem.J. 421: 387


    Organizational Affiliation

    Venetian Institute of Molecular Medicine, Via G. Orus 2, 35129 Padova, Italy. roberto.battistutta@unipd.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
337Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FU9
Query on FU9

Download SDF File 
Download CCD File 
A
3-(cyclopropylamino)-5-{[3-(trifluoromethyl)phenyl]amino}pyrimido[4,5-c]quinoline-8-carboxylic acid
CX-5279
C22 H16 F3 N5 O2
UXZATHOFDZQOMY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FU9IC50: 0.91 nM BINDINGMOAD
FU9IC50: 0.91 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.352α = 90.00
b = 46.184β = 111.51
c = 63.300γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Elettradata collection
SCALAdata scaling
XDSdata reduction
PHASERphasing
SCALAdata processing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Structure summary