Interactions between drugs and proteins occupy a central position during the process of drug discovery and development. Numerous methods have recently been developed for identifying drug–target interactions, but few have been devoted to finding interactions between post-translationally modified proteins and drugs. We presented a machine learning-based method for identifying associations between small molecules and binding-associated S-nitrosylated (SNO-) proteins. Namely, small molecules were encoded by molecular fingerprint, SNO-proteins were encoded by the information entropy-based method, and the random forest was used to train a classifier. Ten-fold and leave-one-out cross validations achieved, respectively, 0.7235 and 0.7490 of the area under a receiver operating characteristic curve. Computational analysis of similarity suggested that SNO-proteins associated with the same drug shared statistically significant similarity, and vice versa. This method and finding are useful to identify drug–SNO associations and further facilitate the discovery and development of SNO-associated drugs.