3NCG

Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor NM-PP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.Keyloun, K.R.Kim, J.E.Bhandari, J.G.Muller, N.R.Verlinde, C.L.White, A.C.Merritt, E.A.Van Voorhis, W.C.Maly, D.J.

(2010) ACS Med Chem Lett 1: 331-335

  • DOI: 10.1021/ml100096t
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The protozoans Cryptosporidium parvum and Toxoplasma gondii are parasites of major health concern to humans. Both parasites contain a group of calcium-dependent protein kinases (CDPKs), which are found in plants and ciliates but not in humans or fung ...

    The protozoans Cryptosporidium parvum and Toxoplasma gondii are parasites of major health concern to humans. Both parasites contain a group of calcium-dependent protein kinases (CDPKs), which are found in plants and ciliates but not in humans or fungi. Here we describe a series of potent inhibitors that target CDPK1 in C. parvum (CpCDPK1) and T. gondii (TgCDPK1). These inhibitors are highly selective for CpCDPK1 and TgCDPK1 over the mammalian kinases SRC and ABL. Furthermore, they are able to block an early stage of C. parvum invasion of HCT-8 host cells, which is similar to their effects on T. gondii invasion of human fibroblasts.


    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., Buckner, F.S., Parsons, M., Hol, W.G., Merritt, E.A., Van Voorhis, W.C.
      (2010) Nat Struct Mol Biol 17: 602

    Organizational Affiliation

    Department of Chemistry, University of Washington.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-domain protein kinase 1A486Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: CDPK1cgd3_920
EC: 2.7.11.17
Find proteins for A3FQ16 (Cryptosporidium parvum (strain Iowa II))
Explore A3FQ16 
Go to UniProtKB:  A3FQ16
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BK1
Query on BK1

Download CCD File 
A
1-(1-methylethyl)-3-(naphthalen-1-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C19 H19 N5
QFGDRGRJMYSRIW-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BK1IC50 :  150   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.991α = 90
b = 55.968β = 104.78
c = 81.972γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-20
    Changes: Data collection
  • Version 1.3: 2017-11-08
    Changes: Refinement description