2PVN

Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2

• PDB DOI: https://doi.org/10.2210/pdb2PVN/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-05-09 Released: 2008-05-13 
• Deposition Author(s): Nie, Z., Perretta, C., Erickson, P., Margosiak, S., Almassy, R., Lu, J., Averill, A., Yager, K.M., Chu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.308 
• R-Value Work: 0.250 
• R-Value Observed: 0.256 

Literature

Structure-based design, synthesis, and study of pyrazolo[1,5-a][1,3,5]triazine derivatives as potent inhibitors of protein kinase CK2.

Nie, Z., Perretta, C., Erickson, P., Margosiak, S., Almassy, R., Lu, J., Averill, A., Yager, K.M., Chu, S.

(2007) Bioorg Med Chem Lett 17: 4191-4195

• PubMed: 17540560 
• DOI: https://doi.org/10.1016/j.bmcl.2007.05.041
• Primary Citation of Related Structures:  
  2PVH, 2PVJ, 2PVK, 2PVL, 2PVM, 2PVN


• PubMed Abstract: 
  

  The structure-based design, synthesis, and anticancer activity of novel inhibitors of protein kinase CK2 are described. Using pyrazolo[1,5-a][1,3,5]triazine as the core scaffold, a structure-guided series of modifications provided pM inhibitors with microM-level cytotoxic activity in cell-based assays with prostate and colon cancer cell lines.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Polaris Pharmaceuticals Inc., San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.83 kDa 
• Atom Count: 2,875 
• Modelled Residue Count: 328 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	352	Zea mays	Mutation(s): 2  Gene Names: ACK2 EC: 2.7.11.1
UniProt
Find proteins for P28523 (Zea mays) Explore P28523  Go to UniProtKB:  P28523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P63	B [auth A]	N-(3-(8-CYANO-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZIN-2-YLAMINO)PHENYL)ACETAMIDE C20 H16 N8 O QVKXQLGRDOMAGC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
P63	PDBBind:  2PVN	Ki: 0.35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.308 
• R-Value Work: 0.250 
• R-Value Observed: 0.256 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.394	α = 90
b = 59.415	β = 103.004
c = 45.819	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-13 
Deposition Author(s): Nie, Z., Perretta, C., Erickson, P., Margosiak, S., Almassy, R., Lu, J., Averill, A., Yager, K.M., Chu, S.

Revision History  

• Version 1.0: 2008-05-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary