O. sanctum L. (O. tenuiflorum) is an important sacred medicinal plant of India known as Holy Basil or Tulsi. The chemical composition of volatile oil is highly complex and comprises high ratio of phenylpropanoids and terpenes, and some phenolic compound or flavonoids such as orientin and vicenin. These minor flavonoids are known to be antioxidant and anticancer in nature. Orientin reported as potential anticancer agent due to anti-proliferative activity on human liver cancer cell line HepG2, but its mechanism of action is not fully explored. In the present work an in-silico structure-activity relationship study on orientin was performed and built a pharmacophore mapping and QSAR model to screen out the potential structurally similar analogues from chemical database of Discovery Studio (DSv3.5, Accelrys, USA) as potential anticancer agent. Analogue fenofibryl glucuronide was selected for in vitro cytotoxic/anticancer activity evaluation through MTT assay. Binding affinity and mode of action of orientin and its analogue were explored through molecular docking studies on quinone oxidoreductase, a potential target of flavonoids. Contrary to the assumption, in vitro results showed only 41% cell death at 202.389 μM concentration (at 96 hrs). Therefore, we concluded that the selected orientin analogue fenofibryl glucuronide was non-cytotoxic/non-anti-carcinogenic up to 100 μg/ml (202.389 μM) concentrations for a long term exposure i.e., till 96 hrs in human cancer cells of HepG2. We concluded that orientin and its analogue fenofibryl glucuronide as pure compound showed no activity or less cytotoxicity activity on liver cancer cell line HepG2.