With its high level of phytochemical and botanical variability, Papaver genus contains several species with many subspecies yielding more than 170 alkaloids. Papaver species have been used as sedative, hypnotic, analgesic, and antidepressant. The aim of this study is to shed light on the structure-activity relationship of alkaloids isolated from Papaver genus. All alkaloids isolated from Papaver genus are listed according to their plant source. We identified the molecular targets of the 92 alkaloids from 10 different types of Papaver alkaloids (simple isoquinoline, benzylisoquinoline, proaporphine, aporphine, morphinane, promorphinane, protoberberine, phthalideisoquinoline, protopine, and rhoeadine) by using cheminformatic approach (Swiss Model). Hierarchical clustering heatmaps were generated by R programming language to visualize the in silico results. The research finding of this study could act as a guiding source for future natural product-based drug discovery.