Structural basis for compound C inhibition of the human AMP-activated protein kinase α2 subunit kinase domain

AMP‐activated protein kinase (AMPK) is a serine/threonine kinase that functions as a sensor to maintain energy balance at both the cellular and the whole‐body levels and is therefore a potential target for drug design against metabolic syndrome, obesity and type 2 diabetes. Here, the crystal structure of the phosphorylated‐state mimic T172D mutant kinase domain from the human AMPK α2 subunit is reported in the apo form and in complex with a selective inhibitor, compound C. The AMPK α2 kinase domain exhibits a typical bilobal kinase fold and exists as a monomer in the crystal. Like the wild‐type apo form, the T172D mutant apo form adopts the autoinhibited structure of the `DFG‐out' conformation, with the Phe residue of the DFG motif anchored within the putative ATP‐binding pocket. Compound C binding dramatically alters the conformation of the activation loop, which adopts an intermediate conformation between DFG‐out and DFG‐in. This induced fit forms a compound‐C binding pocket composed of the N‐lobe, the C‐lobe and the hinge of the kinase domain. The pocket partially overlaps with the putative ATP‐binding pocket. These three‐dimensional structures will be useful to guide drug discovery.