4YJN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00319
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-domain protein kinase 1484Toxoplasma gondiiMutation(s): 0 
Gene Names: CDPK1
UniProt
Find proteins for Q9BJF5 (Toxoplasma gondii)
Explore Q9BJF5 
Go to UniProtKB:  Q9BJF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BJF5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UW4
Query on UW4

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
UW4 BindingDB:  4YJN IC50: min: 5, max: 12 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.3α = 90
b = 72.64β = 99.72
c = 65.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI089441

Revision History  (Full details and data files)

  • 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