5H8G

Crystal structure of CK2 with compound 7b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent and Selective CK2 Kinase Inhibitors with Effects on Wnt Pathway Signaling in Vivo.

Dowling, J.E.Alimzhanov, M.Bao, L.Chuaqui, C.Denz, C.R.Jenkins, E.Larsen, N.A.Lyne, P.D.Pontz, T.Ye, Q.Holdgate, G.A.Snow, L.O'Connell, N.Ferguson, A.D.

(2016) Acs Med.Chem.Lett. 7: 300-305

  • DOI: 10.1021/acsmedchemlett.5b00452
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Wnt pathway is an evolutionarily conserved and tightly regulated signaling network with important roles in embryonic development and adult tissue regeneration. Impaired Wnt pathway regulation, arising from mutations in Wnt signaling components, s ...

    The Wnt pathway is an evolutionarily conserved and tightly regulated signaling network with important roles in embryonic development and adult tissue regeneration. Impaired Wnt pathway regulation, arising from mutations in Wnt signaling components, such as Axin, APC, and β-catenin, results in uncontrolled cell growth and triggers oncogenesis. To explore the reported link between CK2 kinase activity and Wnt pathway signaling, we sought to identify a potent, selective inhibitor of CK2 suitable for proof of concept studies in vivo. Starting from a pyrazolo[1,5-a]pyrimidine lead (2), we identified compound 7h, a potent CK2 inhibitor with picomolar affinity that is highly selectivity against other kinase family enzymes and inhibits Wnt pathway signaling (IC50 = 50 nM) in DLD-1 cells. In addition, compound 7h has physicochemical properties that are suitable for formulation as an intravenous solution, has demonstrated good pharmacokinetics in preclinical species, and exhibits a high level of activity as a monotherapy in HCT-116 and SW-620 xenografts.


    Organizational Affiliation

    Structure & Biophysics, Discovery Sciences, AstraZeneca R&D , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.,Structure & Biophysics, Discovery Sciences, AstraZeneca R&D , Darwin Building, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K.,Oncology Innovative Medicines Unit, AstraZeneca R&D , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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
5Y4
Query on 5Y4

Download SDF File 
Download CCD File 
A
~{N}-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-[2-(dimethylamino)ethyl-methyl-amino]phenyl]ethanamide
C23 H29 N9 O
SRABOMKMQRYXIK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5Y4IC50: <3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.810α = 90.00
b = 78.810β = 90.00
c = 81.880γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-12-23 
  • Released Date: 2016-02-10 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references