Students always encounter difficulties in studying biochemical pathways. They are especially weak in understanding the relationships between metabolic pathways and their integration because these pathways are always taught one-by-one in class. In the past, various online resources have been developed to facilitate students' understanding toward energy metabolism. Although these learning materials enable students to understand individual metabolic pathway in a clearer manner, many of them fail to demonstrate the linkages between these pathways. The "AG City" is a self-learning tool which aims to arouse students' interest in exploring nucleotide metabolism. We have designed a metro map as a concept map to allow students to have an overview of different pathways as well as their integration. Major pathways are presented as railway lines in an easy-to-understand and interactive manner using navigation, animations, and narrations. Key molecules involved in the pathways are presented as "railway stations". Students can easily identify common "railway stations" presented in different pathways and link the concepts that they have learnt together. This interactive self-learning tool has been packaged as a courseware using the Articulate Storyline eLearning authoring software.