Crystal structure of CK2 with compound 7h

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/acsmedchemlett.5b00452
  • Primary Citation of Related Structures:  
    5H8B, 5H8E, 5H8G

  • 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, 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

    Oncology Innovative Medicines Unit, AstraZeneca R&D , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
333Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1CK2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5Y3

Download Ideal Coordinates CCD File 
TA [auth B],
W [auth A]
C21 H25 N9 O
Query on SO4

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AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
D [auth A]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
X [auth B],
Y [auth B],
Z [auth B]
O4 S
Query on EDO

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EA [auth B]
FA [auth B]
GA [auth B]
HA [auth B]
I [auth A]
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
U [auth A],
V [auth A]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
5Y3 BindingDB:  5H8E Kd: 2.50e-4 (nM) from 1 assay(s)
IC50: min: 3, max: 3000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.92α = 90
b = 126.92β = 90
c = 124.57γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2016-07-20
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description