4GRB

Casein kinase 2 (CK2) bound to inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


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


Literature

Structure and Property Based Design of Pyrazolo[1,5-a]pyrimidine Inhibitors of CK2 Kinase with Activity in Vivo.

Dowling, J.E., Alimzhanov, M., Bao, L., Block, M.H., Chuaqui, C., Cooke, E.L., Denz, C.R., Hird, A., Huang, S., Larsen, N.A., Peng, B., Pontz, T.W., Rivard-Costa, C., Saeh, J.C., Thakur, K., Ye, Q., Zhang, T., Lyne, P.D.

(2013) ACS Med Chem Lett 4: 800-805

  • DOI: https://doi.org/10.1021/ml400197u
  • Primary Citation of Related Structures:  
    4GRB

  • PubMed Abstract: 

    • In this letter, we describe the design, synthesis, and structure-activity relationship of 5-anilinopyrazolo[1,5-a]pyrimidine inhibitors of CK2 kinase. Property-based optimization of early leads using the 7-oxetan-3-yl amino group led to a series of matched molecular pairs with lower lipophilicity, decreased affinity for human plasma proteins, and reduced binding to the hERG ion channel ...

    In this letter, we describe the design, synthesis, and structure-activity relationship of 5-anilinopyrazolo[1,5-a]pyrimidine inhibitors of CK2 kinase. Property-based optimization of early leads using the 7-oxetan-3-yl amino group led to a series of matched molecular pairs with lower lipophilicity, decreased affinity for human plasma proteins, and reduced binding to the hERG ion channel. Agents in this study were shown to modulate pAKT(S129), a direct substrate of CK2, in vitro and in vivo, and exhibited tumor growth inhibition when administered orally in a murine DLD-1 xenograft.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alphaA333Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1, CK2A1
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
0XG
Query on 0XG
Download Ideal Coordinates CCD File 
C [auth A]5-(2-{[4-(dimethylcarbamoyl)phenyl]amino}-4-methoxypyrimidin-5-yl)thiophene-3-carboxylic acid
C19 H18 N4 O4 S
HXQTUKJNZNLOBD-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0XG Binding MOAD:  4GRB IC50: 17 (nM) from 1 assay(s)
BindingDB:  4GRB IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.431α = 90
b = 61.897β = 90
c = 116.241γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references