Metabolic pathway databases such as KEGG contain information on thousands of biochemical reactions drawn from the biomedical literature. Ensuring consistency of such large metabolic pathways is essential to their proper use. In this paper, we present a new method to determine consistency of an important class of biochemical reactions. Our method exploits the knowledge of the atomic rearrangement pattern in biochemical reactions, to reduce the automatic atom mapping problem to a series of chemical substructure searches between the substrate and the product of a biochemical reaction. As an illustrative application, we describe the exhaustive validation of a substantial portion from the latest release of the KEGG LIGAND database.