Quercetin is a flavonoid compound that belongs to the flavonol and flavone classes and is found in plants such as the Majapahit tree. The Majapahit plant (Crescentia cujete) is widely distributed across Indonesia, growing in areas such as Makassar, Sumatra, Java, Kalimantan and Ternate. This plant contains alkaloids, flavonoids, saponins, steroids, vitamins, carbohydrates, organic acids, amino acids and minerals. It has antimicrobial, anti-inflammatory, antipyretic, analgesic, anti-fertility, anti-diabetic, anti-lipidemic, cardioprotective and antineoplastic properties. Data analysis of the Majapahit plant fraction using LC-MS has identified quercetin as a flavonoid compound with biological activity, particularly antimicrobial effects. The molecular docking mechanism of quercetin shows that it binds as a ligand to receptors in the form of the DnaK and gyrA proteins, each with affinity values of −9.0 kcal/moll and −7.4 kcal/moll, respectively. Moreover, the interaction involves three types of bonds, van der Waals, hydrogen and carbon-hydrogen, with 19 amino acids involved.