Anthocyanins are an important pharmaceutical ingredient possessing diet regulatory, antioxidant, anticancer, antidiabetic, anti-obesity, antimicrobial, and anti-inflammatory properties. Pelargonidin is an important anthocyanin-based orange-red flavonoid compound used in drugs for treating hypoglycemia, retinopathy, skeletal myopathy, etc. The main sources of pelargonidin are strawberries and food products with red pigmentation. There is a lack of evidence for supporting its use as an independent supplement. In the present study, pelargonidin and pelargonidin-3-O-glucoside are studied for their structural properties using quantum chemical calculations based on density functional theory. The results confirmed that the parent compound and its glycosylated derivative acted as good electron donors. Electrostatic potential, frontier molecular orbitals, and molecular descriptor analyses also substantiated their electron donating properties. Furthermore, based on the probability, a target prediction was performed for pelargonidin and pelargonidin-3-O-glucoside. Hydroxyacyl-coenzyme A dehydrogenase was chosen as an enzymatic target of interest, since the presence work focuses on glucuronidated compounds and their efficacy over diabetes. Possible interactions between these compounds and a target with nominable binding energies were also evaluated. Further, the structural stability of these two compounds were also analyzed using a molecular dynamics simulation.