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

Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates 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 human 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 molecular 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 - using the fpocket and mdpocket packages on MD-generated trajectories. This led to a first categorization 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. This study gives initial insights into the largely uncharted fields plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.