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Figure 1.
Structure and binding orientation of inhibitors that recognize
the Abl/c-Kit–like inactive conformation of protein kinases.
A, schematic representation of the subsites that are occupied
by inhibitors that bind the DFG Asp-out conformation of Abl.
Red, P-loop; orange, helix αC; blue, activation loop.
The three distinct subregions that are occupied by imatinib
(adenine pocket, specificity pocket, and exposed site) are
represented with dotted circles. The letters used to label
imatinib in this model directly correlate to the structure
in B. B, chemical structures of imatinib, DSA1, and DSA8.
All molecules are drawn in an orientation that is consistent
with their mode of binding to c-Src or Abl. Red, functional
groups, which are similar between the inhibitors. Each ring
in these structures is labeled (rings A–F) for reference.
High Resolution PDF
Figure 2.
Structurally defined conformational states of the c-Src and
Abl kinase domains. Red, P-loop; orange, helix αC;
blue, activation loop. State A, active c-Src kinase Thr338Ile
(PDB entry 3DQW; ref. 16); state B, inactive Src/Cdk–like
conformation (PDB entry 1QCF; ref. 32); state C, inactive
Abl/c-Kit–like conformation (PDB entry 1OPJ; 33) with the
DFG motif in the flipped conformation relative to states A and B
High Resolution PDF
Figure 3.
Solvent exposure of inhibitors. Top, structures of the
Abl·imatinib (A, PDB entry 1OPJ; ref. 33), c-Src·imatinib
(B, PDB entry 2OIQ; ref. 3), and Src·DSA8 (C) complexes for
comparison. Transparent gray, the solvent accessible surface
of the proteins; red, P-loop; orange, helix αC; blue,
activation loop. Each ring of imatinib and DSA8 has been
labeled A to F in the structure representation (top) and
the schematic drawing (bottom). Bottom, the solvent
accessible area was calculated for the atoms (red) for
imatinib and DSA8 in each protein complex.
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Table 1.
In vitro activities of DSA1-DSA9 and imatinib against
Abl, c-Src, and Hck
Note: All assays were performed in triplicate or quadruplicate.
Figure 4.
Structures of wt c-Src·imatinib (A, PDB-entry 2OIQ; ref.
3), wt c-Src·DSA8 (B), and Thr338Ile c-Src·DSA1 (C). In
all three complexes, c-Src is in an Abl/c-Kit–like
inactive conformation with a flipped DFG motif. Top,
structure of the active site region of these complexes.
c-Src is shown in gray ribbons. Red, P-loop; orange, helix
αC; blue, DFG motif. Parts of the protein that
obscure the view of the inhibitors have been removed
for clarity. Each ring in DSA1, DSA8, and imatinib has
been labeled according to Fig. 1B. Bottom, schematic
diagram of the binding interactions made by DSA1, DSA8,
and imatinib with c-Src. Red semicircles, hydrophobic
contacts; green dotted lines, H bonds with their
respective lengths. The yellow arrow in the depiction of
DSA1 and DSA8 indicates the rotation of ring D relative
to imatinib. Schematic drawings were prepared with
LigPlot (34). D, proliferation of parental Ba/F3 cells
in the presence of IL-3 and Ba/F3 BCR-ABL cells and in
the absence of IL-3 in response to a dose titration of
DSA8. Error bars, SEM.
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