4GRB

Casein kinase 2 (CK2) bound to inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GRB/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-24 Released: 2013-08-28 
• Deposition Author(s): Larsen, N.A., Dowling, J.E., Ferguson, A.D.

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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 

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

• PubMed: 24900749 
• 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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.31 kDa 
• Atom Count: 2,969 
• Modelled Residue Count: 327 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	333	Homo sapiens	Mutation(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 GTEx:  ENSG00000101266

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XG	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
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 49.431	α = 90
b = 61.897	β = 90
c = 116.241	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Larsen, N.A., Dowling, J.E., Ferguson, A.D.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations