4YJN | pdb_00004yjn

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1639

• PDB DOI: https://doi.org/10.2210/pdb4YJN/pdb

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


• Deposited: 2015-03-03 Released: 2015-11-25 
• Deposition Author(s): Merritt, E.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

SAR Studies of 5-Aminopyrazole-4-carboxamide Analogues as Potent and Selective Inhibitors of Toxoplasma gondii CDPK1.

Huang, W., Ojo, K.K., Zhang, Z., Rivas, K., Vidadala, R.S., Scheele, S., DeRocher, A.E., Choi, R., Hulverson, M.A., Barrett, L.K., Bruzual, I., Siddaramaiah, L.K., Kerchner, K.M., Kurnick, M.D., Freiberg, G.M., Kempf, D., Hol, W.G., Merritt, E.A., Neckermann, G., de Hostos, E.L., Isoherranen, N., Maly, D.J., Parsons, M., Doggett, J.S., Van Voorhis, W.C., Fan, E.

(2015) ACS Med Chem Lett 6: 1184-1189

• PubMed: 26693272 
• DOI: https://doi.org/10.1021/acsmedchemlett.5b00319
• Primary Citation Related Structures: 
  4YJN


• PubMed Abstract: 
  

  We previously discovered compounds based on a 5-aminopyrazole-4-carboxamide scaffold to be potent and selective inhibitors of CDPK1 from T. gondii . The current work, through structure-activity relationship studies, led to the discovery of compounds ( 34 and 35 ) with improved characteristics over the starting inhibitor 1 in terms of solubility, plasma exposure after oral administration in mice, or efficacy on parasite growth inhibition. Compounds 34 and 35 were further demonstrated to be more effective than 1 in a mouse infection model and markedly reduced the amount of T. gondii in the brain, spleen, and peritoneal fluid, and 35 given at 20 mg/kg eliminated T. gondii from the peritoneal fluid.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.
Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States.
Department of Chemistry, University of Washington , Seattle, Washington 98195, United States.
Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109, United States.
Portland VA Medical Center , Portland, Oregon 97239, United States.
AbbVie , N. Chicago, Illinois 60064, United States.
PATH , San Francisco, California 94102, United States.
Department of Pharmaceutics, University of Washington , Seattle, Washington 98195, United States.
Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109, United States ; Department of Global Health, University of Washington , Seattle, Washington 98195, United States.
Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States ; Department of Global Health, University of Washington , Seattle, Washington 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: 55.61 kDa 
• Atom Count: 3,764 
• Modeled Residue Count: 460 
• 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: CDPK1 EC: 2.7.11.1
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
UW4	B [auth A]	5-amino-1-tert-butyl-3-[2-(cyclobutyloxy)quinolin-6-yl]-1H-pyrazole-4-carboxamide C21 H25 N5 O2 BTTULLMSRICKGC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.3	α = 90
b = 72.64	β = 99.72
c = 65.71	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Merritt, E.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI089441

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2016-01-06
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description