Models of the wild-type and gatekeeper mutants of Hck in the presence of the ATP analog, AMP-PNP, and the inhibitor, NaPP1. A) Chemical structures of AMP-PNP and NaPP1. B) Molecular model of downregulated Hck bound to AMP-PNP. The overall structure (left) shows the SH3 domain (red), the SH2 domain (blue), and the kinase domain (green). The active site is boxed, and enlarged on the right. The upper right view shows the juxtaposition of the wild-type (WT) gatekeeper residue (T338) with AMP-PNP; the view on the lower right shows the gatekeeper mutant in which Thr338 is replaced with alanine (TA). This model was produced by docking the structure of Hck-YEEI (1QCF)  onto an earlier structure of Hck bound to AMP-PNP (1AD5) . C) Model of Hck bound to NaPP1. The overall structure is shown on the left, and is color-coded as in Part B. Close-up views of the NaPP1 binding site are shown on the right. Note that NaPP1 clashes with the side chain of the gatekeeper residue in this model (arrow; upper right), but this is relieved in the TA mutant (lower right). While the gatekeeper substitution relieves one potential steric clash with the naphthyl moiety of NaPP1, other structural changes are likely to be required to accommodate inhibitor binding. For example, the side chain of the alanine residue immediately adjacent to the DFG motif (Ala403; not shown) also clashes with NaPP1, but this clash could be relieved by movement of the DFG motif to the "out" conformation associated with kinase activation. In this case, the hydrophobic cavity would be enlarged and better able to accommodate the naphthyl moiety of NaPP1 in a horizontal orientation relative to the model shown in Figure 1C. Ultimately, an X-ray crystal structure of Hck-TA with NaPP1 bound will be required to fully understand the inhibitory mechanism. This model was produced using the crystal coordinates for Hck-YEEI bound to PP1 (1QCF) , and docking the NaPP1 structure onto the pyrazolopyrimdine moiety of PP1.
Pene-Dumitrescu et al. BMC Chemical Biology 2012 12:1 doi:10.1186/1472-6769-12-1