3BE9

Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities

• PDB DOI: https://doi.org/10.2210/pdb3BE9/pdb

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


• Deposited: 2007-11-16 Released: 2008-11-18 
• Deposition Author(s): Nie, Z., Perretta, C., Erickson, P., Margosiak, S., Lu, J., Averill, A., Almassy, R., Chu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 

Starting Model: experimental

Literature

Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities.

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

(2008) Bioorg Med Chem Lett 18: 619-623

• PubMed: 18055206 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.074
• Primary Citation of Related Structures:  
  3BE9


• PubMed Abstract: 
  

  A series of macrocyclic derivatives has been designed and synthesized based on the X-ray co-crystal structures of pyrazolo[1,5-a] [1,3,5]triazines with corn CK2 (cCK2) protein. Bioassays demonstrated that these macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds are potent CK2 inhibitors with K(i) around 1.0 nM and strongly inhibit cancer cell growth with IC(50) as low as approximately 100 nM.

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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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.81 kDa 
• Atom Count: 3,007 
• 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): 1  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
P04	B [auth A]	19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one C19 H21 N7 O HIJNSOUPEZHEMC-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
P04	PDBBind:  3BE9	Ki: 24 (nM) from 1 assay(s)
	BindingDB:  3BE9	Ki: 24 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.327	α = 90
b = 59.578	β = 103.419
c = 44.835	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Nie, Z., Perretta, C., Erickson, P., Margosiak, S., Lu, J., Averill, A., Almassy, R., Chu, S.

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-10-30
  Changes: Structure summary