Molecular polypharmacological studies have gained more and more attention as they are important in predicting drug off-target properties and potential toxicity/side effect. The explosive growth of biomedical data provides us an opportunity to develop novel strategies to conduct such studies by analyzing molecular interaction networks. In this paper, we present an integrated web application that is implemented based on more than 5,000 drugs and 56,000 biological macromolecule structures. With efficient search of drug information (biological targets, pharmacology, side effect, etc.) and chemical similarity, molecular maps can be constructed to demonstrate the relationships among multiple drugs and receptors. In addition, receptor information can also be employed to map the interaction network. The 3D structures of available drug-receptor complexes can be visualized via our web server, and the query results will be used to identify similar structures for any given drugs as well as their cross interactions with other biological targets. Our implementation provides an efficient way to evaluate the safety and polypharmacological properties of chemical compounds.