SKiD: A Structure-Oriented Kinetics Database of Enzyme-Substrate Interactions

Abstract

Enzymes are essential biological catalysts that drive nearly all biochemical reactions. Understanding their efficiency and specificity involves studying enzyme kinetics, particularly the parameters kcat and Km. However, there is limited data linking these kinetic parameters with the three-dimensional (3D) structures of enzyme-substrate complexes. Since enzyme function is determined by its structure, such mapping enhances insight into structural basis of enzymatic function and supports applications in enzyme design, synthetic biology and metabolic engineering. To address this critical gap, this work presents SKiD (Structure-oriented Kinetics Database), a comprehensive, structured database integrating kcat and Km values with the corresponding 3D structural data. This is accomplished by integrating data from existing bioinformatics resources using automated programs to process the data and enhancing it with computational predictions. The erroneous data encountered during data integration is manually resolved. Metadata such as literature and assay conditions (e.g., pH and temperature) are preserved. The 3D coordinates of the modelled enzyme-substrate complexes are provided along with their UniProtKB identifier. The database is freely accessible from: https://doi.org/10.5281/zenodo.15355031.