6BFA

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1553


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Development of an Orally Available and Central Nervous System (CNS) Penetrant Toxoplasma gondii Calcium-Dependent Protein Kinase 1 (TgCDPK1) Inhibitor with Minimal Human Ether-a-go-go-Related Gene (hERG) Activity for the Treatment of Toxoplasmosis.

Vidadala, R.S.Rivas, K.L.Ojo, K.K.Hulverson, M.A.Zambriski, J.A.Bruzual, I.Schultz, T.L.Huang, W.Zhang, Z.Scheele, S.DeRocher, A.E.Choi, R.Barrett, L.K.Siddaramaiah, L.K.Hol, W.G.Fan, E.Merritt, E.A.Parsons, M.Freiberg, G.Marsh, K.Kempf, D.J.Carruthers, V.B.Isoherranen, N.Doggett, J.S.Van Voorhis, W.C.Maly, D.J.

(2016) J Med Chem 59: 6531-6546

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00760
  • Primary Citation of Related Structures:  
    4TZR, 6BFA

  • PubMed Abstract: 

    New therapies are needed for the treatment of toxoplasmosis, which is a disease caused by the protozoan parasite Toxoplasma gondii. To this end, we previously developed a potent and selective inhibitor (compound 1) of Toxoplasma gondii calcium-dependent protein kinase 1 (TgCDPK1) that possesses antitoxoplasmosis activity in vitro and in vivo. Unfortunately, 1 has potent human ether-a-go-go-related gene (hERG) inhibitory activity, associated with long Q-T syndrome, and consequently presents a cardiotoxicity risk. Here, we describe the identification of an optimized TgCDPK1 inhibitor 32, which does not have a hERG liability and possesses a favorable pharmacokinetic profile in small and large animals. 32 is CNS-penetrant and highly effective in acute and latent mouse models of T. gondii infection, significantly reducing the amount of parasite in the brain, spleen, and peritoneal fluid and reducing brain cysts by >85%. These properties make 32 a promising lead for the development of a new antitoxoplasmosis therapy.


  • Organizational Affiliation

    Department of Chemistry, 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
EC: 2.7.11.17
UniProt
Find proteins for A0A0F7UUA6 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A0F7UUA6 
Go to UniProtKB:  A0A0F7UUA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7UUA6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UW5
Query on UW5

Download Ideal Coordinates CCD File 
B [auth A]1-{4-amino-3-[6-(cyclopropyloxy)naphthalen-2-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}-2-methylpropan-2-ol
C22 H23 N5 O2
NYCAEKAKFOSFFT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UW5 BindingDB:  6BFA IC50: 1 (nM) from 1 assay(s)
EC50: 430 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.124α = 90
b = 72.655β = 99.78
c = 65.746γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

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 StatesR01AI089441

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description