4ONA

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1517

• PDB DOI: https://doi.org/10.2210/pdb4ONA/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-28 Released: 2014-03-19 
• Deposition Author(s): Merritt, E.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Potent and selective inhibitors of CDPK1 from T. gondii and C. parvum based on a 5-aminopyrazole-4-carboxamide scaffold.

Zhang, Z., Ojo, K.K., Vidadala, R., Huang, W., Geiger, J.A., Scheele, S., Choi, R., Reid, M.C., Keyloun, K.R., Rivas, K., Siddaramaiah, L.K., Comess, K.M., Robinson, K.P., Merta, P.J., Kifle, L., Hol, W.G., Parsons, M., Merritt, E.A., Maly, D.J., Verlinde, C.L., Van Voorhis, W.C., Fan, E.

(2014) ACS Med Chem Lett 5: 40-44

• PubMed: 24494061 
• DOI: https://doi.org/10.1021/ml400315s
• Primary Citation of Related Structures:  
  4M84, 4ONA


• PubMed Abstract: 
  

  5-Aminopyrazole-4-carboxamide was used as an alternative scaffold to substitute for the pyrazolopyrimidine of a known "bumped kinase inhibitor" to create selective inhibitors of calcium-dependent protein kinase-1 from both Toxoplasma gondii and Cryptosporidium parvum . Compounds with low nanomolar inhibitory potencies against the target enzymes were obtained. The most selective inhibitors also exhibited submicromolar activities in T. gondii cell proliferation assays and were shown to be non-toxic to mammalian cells.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA 98195, 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: 55.58 kDa 
• Atom Count: 3,796 
• Modelled Residue Count: 465 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-domain protein kinase 1	A	484	Toxoplasma gondii	Mutation(s): 0  Gene Names: AAG53993, CDPK1, TGVEG_042030 EC: 2.7.11.17
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii) Explore Q9BJF5  Go to UniProtKB:  Q9BJF5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UW1	B [auth A]	5-amino-1-tert-butyl-3-(7-ethoxyquinolin-3-yl)-1H-pyrazole-4-carboxamide C19 H23 N5 O2 XZLFLNWUBLMFQW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.27	α = 90
b = 72.631	β = 102.36
c = 67.2	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Merritt, E.A.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description