3V5P

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with inhibitor UW1288


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Multiple Determinants for Selective Inhibition of Apicomplexan Calcium-Dependent Protein Kinase CDPK1.

Ojo, K.K.Murphy, R.C.Johnson, S.M.Zhang, Z.Kim, J.E.Leibly, D.J.Fox, A.M.Reid, M.C.Dale, E.J.Perera, B.G.Kim, J.Hewitt, S.N.Hol, W.G.Verlinde, C.L.Fan, E.Van Voorhis, W.C.Maly, D.J.Merritt, E.A.Larson, E.T.

(2012) J.Med.Chem. 55: 2803-2810

  • DOI: 10.1021/jm201725v
  • Primary Citation of Related Structures:  3SX9, 3SXF, 3T3U, 3T3V, 3UPX, 3UPZ, 3UQF, 3UQG, 3V51, 3V5T
  • Also Cited By: 4JBV, 4M84, 4ONA, 4TZR, 4WG3, 4WG4, 4WG5, 4Y5Q, 6BFA

  • PubMed Abstract: 
  • Diseases caused by the apicomplexan protozoans Toxoplasma gondii and Cryptosporidium parvum are a major health concern. The life cycle of these parasites is regulated by a family of calcium-dependent protein kinases (CDPKs) that have no direct homolo ...

    Diseases caused by the apicomplexan protozoans Toxoplasma gondii and Cryptosporidium parvum are a major health concern. The life cycle of these parasites is regulated by a family of calcium-dependent protein kinases (CDPKs) that have no direct homologues in the human host. Fortuitously, CDPK1 from both parasites contains a rare glycine gatekeeper residue adjacent to the ATP-binding pocket. This has allowed creation of a series of C3-substituted pyrazolopyrimidine compounds that are potent inhibitors selective for CDPK1 over a panel of human kinases. Here we demonstrate that selectivity is further enhanced by modification of the scaffold at the C1 position. The explanation for this unexpected result is provided by crystal structures of the inhibitors bound to CDPK1 and the human kinase c-SRC. Furthermore, the insight gained from these studies was applied to transform an alternative ATP-competitive scaffold lacking potency and selectivity for CDPK1 into a low nanomolar inhibitor of this enzyme with no activity against SRC.


    Related Citations: 
    • Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors
      Ojo, K.K.,Larson, E.T.,Keyloun, K.R.,Castaneda, L.J.,Derocher, A.E.,Inampudi, K.K.,Kim, J.E.,Arakaki, T.L.,Murphy, R.C.,Zhang, L.,Napuli, A.J.,Maly, D.J.,Verlinde, C.L.M.J.,Buckner, F.S.,Parsons, M.,Hol, W.G.J.,Merritt, E.A.,Van Voorhis, W.C.
      (2010) Nat.Struct.Mol.Biol. 17: 602
    • Discovery of potent and selective inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii
      Murphy, R.C.,Ojo, K.K.,Larson, E.T.,Castellanos-Gonzalez, A.,Perera, B.G.K.,Keyloun, K.R.,Kim, J.E.,Bhandari, J.G.,Muller, N.,Verlinde, C.L.M.J.,Nakazawa, S.H.,Hol, W.G.J.,Buckner, F.S.,Napuli, A.J.,White, C.A.,Merritt, E.A.,Van Voorhis, W.C.,Maly, D.J.
      (2010) ACS Med.Chem.Lett. 1: 331


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-domain protein kinase 1
A
484Toxoplasma gondiiGene Names: CDPK1
Find proteins for Q9BJF5 (Toxoplasma gondii)
Go to UniProtKB:  Q9BJF5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C88
Query on C88

Download SDF File 
Download CCD File 
A
3-(4-methoxy-3-methylphenyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C19 H24 N6 O
MQULVMDBNSSIMR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C88Ki: 11 nM BINDINGMOAD
C88Ki: 1.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.160α = 90.00
b = 73.510β = 100.28
c = 66.770γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references