3N51

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor RM-1-95


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
  • Also Cited By: 3V5T, 3V5P, 3V51, 3UQG, 3UQF, 3UPZ, 3UPX, 3T3V, 3T3U, 3SXF, 3SX9, 3I7C, 3I79

  • 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 1
A
484Toxoplasma gondiiMutation(s): 0 
Gene Names: CDPK1
Find proteins for Q9BJF5 (Toxoplasma gondii)
Go to UniProtKB:  Q9BJF5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
BK3
Query on BK3

Download SDF File 
Download CCD File 
A
3-(naphthalen-1-ylmethyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C22 H24 N6
MMRLNUFECMEMSQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BK3IC50: 15 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.523α = 90.00
b = 72.754β = 98.88
c = 66.024γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
Blu-Icedata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description