Data for: A computational pipeline for observing the flexibility and dynamics of (plant) cytochrome P450 binding sites

Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate sub-strates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on hu-man CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use mo-lecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - us-ing the fpocket and mdpocket packages on MD-generated trajectories. This led to the categoriza-tion of 15 chosen plant CYPs based on their binding site’s (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. The results of this study lead a way to evaluate the substrate specificity of plant CYPs and to describe their interactions more precisely. It offers new insights into the structural and functional dynamics of plant CYPs, facili-tating the development of CYP-targeted applications in biotechnology and agriculture. Addition-ally, it serves as a reference for future structural-functional analyses of CYP enzymes across vari-ous biological kingdoms.