Crystal Structure of the Kinase Domain of ABL in Complex with a Potent Rationally-Designed Derivative of the PP1 Inhibitor, AB129

Abstract

As part of our effort to understand the determinants of drug binding to the Abl tyrosine kinase, we determined the crystal structure of the Abl kinase domain bound to a derivative of the PP1 nucleoside analog. Just as the cancer drug imatinib selectively inhibits the tyrosine kinase activity of c-Abl, c-Kit, and the PDGF receptor, but is a poor inhibitor of the closely related Src kinases (1), PP1 is a selective inhibitor of the Src family (2), c-Kit (3), and PDGFR kinases but not of Abl tyrosine kinase activity (3, 4). In fact, PP1 is 1000X less effective at inhibiting Abl and Bcr-Abl kinases than at inhibiting the Src kinases (3, 4). We rationally designed a derivative of the PP1 compound to introduce hydrogen bonding between it and a strictly conserved lysine residue that coordinates the alpha and beta phosphate groups of ATP in protein kinases (5). By expanding the interactions between the inhibitor and Abl kinase, we sought to make the PP1 derivative, AB129, less selective. Our crystal structure of the Abl kinase domain bound to the AB129 inhibitor shows three important features. First, the compound binds to the kinase domain in the active conformation: alpha C helix is rotated inward facilitating a salt bridge between Lys271 and Glu286 and the conserved Asp-Phe-Gly (DFG) motif is oriented Asp-In. In contrast, the structure of PP1 bound to the Src family kinase Hck is in the inactive conformation (6). Second, the strictly conserved Glu286 residue, not Lys271, hydrogen bonds to the hydroxyl group of AB129. Third, the conformation of the phosphate binding loop (P-loop) is extended. We provide kinetic and calorimetric data to support our rationale for the observed conformational changes.