4MX9

CDPK1 from Neospora caninum in complex with inhibitor UW1294


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Neospora caninum Calcium-Dependent Protein Kinase 1 Is an Effective Drug Target for Neosporosis Therapy.

Ojo, K.K.Reid, M.C.Kallur Siddaramaiah, L.Muller, J.Winzer, P.Zhang, Z.Keyloun, K.R.Vidadala, R.S.Merritt, E.A.Hol, W.G.Maly, D.J.Fan, E.Van Voorhis, W.C.Hemphill, A.

(2014) PLoS One 9: e92929-e92929

  • DOI: https://doi.org/10.1371/journal.pone.0092929
  • Primary Citation of Related Structures:  
    4M97, 4MX9, 4MXA

  • PubMed Abstract: 

    Despite the enormous economic importance of Neospora caninum related veterinary diseases, the number of effective therapeutic agents is relatively small. Development of new therapeutic strategies to combat the economic impact of neosporosis remains an important scientific endeavor. This study demonstrates molecular, structural and phenotypic evidence that N. caninum calcium-dependent protein kinase 1 (NcCDPK1) is a promising molecular target for neosporosis drug development. Recombinant NcCDPK1 was expressed, purified and screened against a select group of bumped kinase inhibitors (BKIs) previously shown to have low IC50s against Toxoplasma gondii CDPK1 and T. gondii tachyzoites. NcCDPK1 was inhibited by low concentrations of BKIs. The three-dimensional structure of NcCDPK1 in complex with BKIs was studied crystallographically. The BKI-NcCDPK1 structures demonstrated the structural basis for potency and selectivity. Calcium-dependent conformational changes in solution as characterized by small-angle X-ray scattering are consistent with previous structures in low Calcium-state but different in the Calcium-bound active state than predicted by X-ray crystallography. BKIs effectively inhibited N. caninum tachyzoite proliferation in vitro. Electron microscopic analysis of N. caninum cells revealed ultra-structural changes in the presence of BKI compound 1294. BKI compound 1294 interfered with an early step in Neospora tachyzoite host cell invasion and egress. Prolonged incubation in the presence of 1294 interfered produced observable interference with viability and replication. Oral dosing of BKI compound 1294 at 50 mg/kg for 5 days in established murine neosporosis resulted in a 10-fold reduced cerebral parasite burden compared to untreated control. Further experiments are needed to determine the PK, optimal dosage, and duration for effective treatment in cattle and dogs, but these data demonstrate proof-of-concept for BKIs, and 1294 specifically, for therapy of bovine and canine neosporosis.


  • Organizational Affiliation

    Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-like domain protein kinase isoenzyme gamma, related485Neospora caninum LiverpoolMutation(s): 0 
Gene Names: CDPK1NCLIV_011980XP_003880764
EC: 2.7.11.17
UniProt
Find proteins for F0V9W9 (Neospora caninum (strain Liverpool))
Explore F0V9W9 
Go to UniProtKB:  F0V9W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF0V9W9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2E8
Query on 2E8

Download Ideal Coordinates CCD File 
B [auth A]3-(6-ethoxynaphthalen-2-yl)-1-[(1-methylpiperidin-4-yl)methyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C24 H28 N6 O
KONPIFGGWNMOKY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2E8 BindingDB:  4MX9 IC50: min: 2.9, max: 3 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.38α = 90
b = 73.141β = 99.84
c = 66.27γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description