CBR-db: A Cheminformatic Database for Biochemical Reaction Analysis

We present CBR-db, a database with detailed chemical properties data for biochemical compounds and reactions. We provide the first chemically consistent analyses and detailed chemical property data for a biologically relevant set of 148,673 reactions and 18,716 small molecules derived from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the ATLAS of Biochemistry. CBR-db provides detailed atom tracking, reaction similarity classification, compound properties, chiral centers, molecular assembly indices, and thermodynamic properties. CBR-db is designed to be continuously updated, open-source, and reproducible. This report highlights the cheminformatic data, explains the curation and data set, and highlights the data's utility for researchers working at the intersection of chemical properties and biology. We anticipate a broad range of potential applications for these data, given their position at the intersection of cheminformatics and bioinformatics, including researchers interested in molecular properties and reaction mechanisms found in metabolism, the chemical underpinnings of synthetic biochemical design and engineering, and how the origins and evolution of biochemistry have selected among properties of molecules and reactions within chemical space.