FR258900 has been discovered as a novel inhibitor of human liver glycogen phosphorylase a and proved to suppress hepatic glycogen breakdown and reduce plasma glucose concentrations in diabetic mice models. To elucidate the mechanism of inhibition, we have determined the crystal structure of the cocrystallized rabbit muscle glycogen phosphorylase b-FR258900 complex and refined it to 2.2 Å resolution. The structure demonstrates that the inhibitor binds at the allosteric activator site, where the physiological activator AMP binds. The contacts from FR258900 to glycogen phosphorylase are dominated by nonpolar van der Waals interactions with Gln71, Gln72, Phe196, and Val459 (from the symmetry-related subunit), and also by ionic interactions from the carboxylate groups to the three arginine residues (Arg242, Arg309, and Arg310) that form the allosteric phosphate-recognition subsite. The binding of FR258900 to the protein promotes conformational changes that stabilize an inactive T-state quaternary conformation of the enzyme. The ligand-binding mode is different from those of the potent phenoxy-phthalate and acyl urea inhibitors, previously described, illustrating the broad specificity of the allosteric site.Keywords: FR258900; glycogen phosphorylase; inhibition; X-ray crystallography; type 2 diabetes Inhibition of glycogenolysis has been proposed as a therapeutic strategy for the treatment of type 2 diabetes. Glycogen phosphorylase (GP) catalyzes the first step in glycogen degradation, and it is expected that inhibition of GP will inhibit glycogenolysis, reduce hepatic glucose production, and lower blood glucose, thereby providing a potential new treatment for type 2 diabetes (McCormack et al. 2001;Treadway et al. 2001;Sarabu and Tilley 2005;Baker et al. 2006). GP is physiologically regulated through small molecule allosteric effectors as well as through phosphorylation at Ser14, resulting in a structural switch between active (R-state) and inactive (T-state) conformation (for a review, see Johnson et al. 1989;Johnson 1992;Oikonomakos et al. 1992). Several binding sites on the enzyme such as the catalytic, allosteric, inhibitor, and the new allosteric site have been identified as specific targets for inhibitor binding (for a review, see Oikonomakos 2002).The allosteric site, which binds the activator AMP (Barford et al. 1991;Sprang et al. 1991) Abbreviations: GP, glycogen phosphorylase; 1,4-a-D-glucan, orthophosphate a-glucosyltransferase (EC 2.4.1.1); rmGPb, rabbit muscle glycogen phosphorylase b; rmGPa, rabbit muscle glycogen phosphorylase a; hlGPa, human liver glycogen phosphorylase a; PLP, pyridoxal 59-phosphate; glucose, a-D-glucose; Glc-1-P, a-D-glucose 1-phosphate; Glc-6-P, D-glucose 6-phosphate; FR258900, (2R,3S) 2,3-bis((E)-3-(4-hydroxyphenyl) acryloyloxy) pentanedioic acid; W1807, (À)(S)-3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5,6-tricarboxylate; compound 4j, 4-[2,4-Bis-(3-nitrobenzoylamino) phenoxy]phthalic acid; compound 21, 1-(2-chloro-4-fluorobenzoyl)-3-(5-hydroxy-...