The Escherichia coli metabolome has been characterised using the two-dimensional structures of 745 metabolites, obtained from the EcoCyc and KEGG databases. Physicochemical properties of the metabolome have been calculated to provide an overview of this set of cognate ligands. A library of fragments commonly found among these molecules has been employed to reveal the main constituents of metabolites, and to assist a broad classification of the metabolome into biochemically relevant classes. Fragment-based fingerprints reveal the metabolome as a continuum in the two-dimensional structural space, where clusters of molecules sharing similar scaffolds can be identified, but are generally overlapping. Nucleotide, carbohydrate and amino acid-like molecules are the most prominent, but at high levels of similarity, a more detailed classification is possible. Classification schemes for the metabolome are a promising tool for understanding the chemical diversity of the metabolome. When used in conjunction with existing classifications of the proteome, they can help to elucidate the binding preferences and promiscuity of proteins and their cognate substrates.