Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder and its concurrent presence with chronic kidney disease (CKD) is a significant concern. Glycerol kinase (GK) and glycerol 3-phosphate shuttle enzymes (cGPDH and mGPDH) facilitate the regulation of endogenous glucose production in many cell lines. This research investigates the functions of GK, cGPDH, and mGPDH in HEK293 cells. Standard protocols were employed to assess enzyme activity, mRNA- and protein-expression, glucose uptake, and production. Homology modeling and molecular docking were employed to elucidate interactions of genistein and metformin with these enzymes. The secondary structures of GK, cGPDH and mGPDH and the thermal stability of cGPDH and mGPDH were analyzed by CD spectra. Genistein inhibited GK activity by 40%, while metformin decreased cGPDH and mGPDH activity by 58% and 55%, respectively, in HEK293 cells. Nonetheless, the expression levels of mRNA and protein remained unaltered. Genistein and metformin inhibited HEK293 glucose production by 0.46-fold and 0.63-fold, respectively. Genistein reduced glucose uptake by 0.26-fold, while metformin increased it by 0.51-fold. Genistein allosterically interacted with GK with a CDocker energy of -27.71, while metformin interacted with Gln295 and Lys296 of the catalytic loop of cGPDH and the FAD