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

Experimental Data Snapshot

  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/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. 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src
A, B
286Gallus gallusMutation(s): 0 
Gene Names: SRC
Find proteins for P00523 (Gallus gallus)
Explore P00523 
Go to UniProtKB:  P00523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BK5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H21 N5 O
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)
PDBBind:  3UQF Ki: 2.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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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
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations