Crystal structure of c-Src in complex with pyrazolopyrimidine 3

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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Small molecule recognition of c-Src via the Imatinib-binding conformation.

Dar, A.C.Lopez, M.S.Shokat, K.M.

(2008) Chem Biol 15: 1015-1022

  • DOI: https://doi.org/10.1016/j.chembiol.2008.09.007
  • Primary Citation of Related Structures:  
    3EL7, 3EL8

  • PubMed Abstract: 

    The cancer drug, Imatinib, is a selective Abl kinase inhibitor that does not inhibit the closely related kinase c-Src. This one drug and its ability to selectively inhibit Abl over c-Src has been a guiding principle in virtually all kinase drug discovery efforts in the last 15 years. A prominent hypothesis explaining the selectivity of Imatinib is that Abl has an intrinsic ability to adopt an inactive conformation (termed DFG-out), whereas c-Src appears to pay a high intrinsic energetic penalty for adopting this conformation, effectively excluding Imatinib from its ATP pocket. This explanation of the difference in binding affinity of Imatinib for Abl versus c-Src makes the striking prediction that it would not be possible to design an inhibitor that binds to the DFG-out conformation of c-Src with high affinity. We report the discovery of a series of such inhibitors. We use structure-activity relationships and X-ray crystallography to confirm our findings. These studies suggest that small molecules are capable of inducing the generally unfavorable DFG-out conformation in c-Src. Structural comparison between c-Src in complex with these inhibitors allows us to speculate on the differential selectivity of Imatinib for c-Src and Abl.

  • Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, Genentech Hall, 600 16(th) Street, University of California, San Francisco, San Francisco, CA 94158, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene tyrosine-protein kinase Src286Gallus 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 PD3

Download Ideal Coordinates CCD File 
B [auth A]1-{3-[(4-amino-1-cyclopentyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)methyl]phenyl}-3-[3-(trifluoromethyl)phenyl]urea
C25 H24 F3 N7 O
Binding Affinity Annotations 
IDSourceBinding Affinity
PD3 PDBBind:  3EL7 IC50: 480 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.36α = 90
b = 63.13β = 91.9
c = 56.05γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-07
    Changes: Database references
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description