Cancer are caused by abnormalities in the genetic material of the transformed cells. The study aims to analyze active the chemical compounds from the n-hexane and chloroform fractionates of eceng gondok and to know the interaction between the compounds a target with DNA enzyme topoisomerase as receptor with molecular docking. The compounds analysis was carried out by gas chromatography-mass spectrometry (GC-MS). GC-MS analysis showed various compounds are present in the n-hexane fraction, comprising 2-pyridinepropanoic acid, .alpha.-methyl-.beta.-oxo-, ethyl ester; acetic acid, hydrazide; hydrazine, (1,1-dimethylethyl); hydroperoxide, 1-ethylbutyl; dan hydroperoxide, 1-methylpentyl. Whereas, in the chloroform fractions 2-pyridinepropanoic acid, .alpha.-methyl-.beta.-oxo-, ethyl ester; 2-oxazolidinethione, 5-[2-(methylthio)ethyl]; carbamic acid, methyl ester; (Z)-1-(ethoxycarbonyl-1-fluoro-2-(methoxycarbonyl)-1,3-butadiene; and carbamic acid, methyl ester were found. The method validation showed RMSD value of <2.5 Å, the ligand binding interactions showed that 2-pyridinepropanoic acid, .alpha.-methyl-.beta.-oxo-, ethyl ester; acetic acid, hydrazide and carbamic acid, methyl ester from n-hexane and chloroform had a lowest energy binding. However, the compound from the n-hexane and chloroform fractions showed no apparent interaction with DNA topoisomerase.