3UQF

c-SRC kinase domain in complex with BKI RM-1-89


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

Larson, E.T.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.

(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, 3V5P, 3V5T

  • 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 homologues in the human host ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase SrcA, B286Gallus gallusMutation(s): 0 
Gene Names: SRC
EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BK5 (Subject of Investigation/LOI)
Query on BK5

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]3-(6-ethoxynaphthalen-2-yl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C20 H21 N5 O
MJOCJDMQRCJQJF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
BK5 BindingDB:  3UQF Ki: 200 (nM) from 1 assay(s)
IC50: min: 200, max: 549 (nM) from 3 assay(s)
Binding MOAD:  3UQF Ki: 200 (nM) from 1 assay(s)
PDBBind:  3UQF Ki: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.79α = 79.32
b = 63.24β = 89.35
c = 73.3γ = 89.88
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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