This data set contains the raw data used for the preparation of the manuscript 'Key structural features, thermodynamics and kinetics along the pathway between active and inactive forms of thrombin'. It is separated into following parts: X-ray: Data used in the analysis of the PDB structures of thrombin, including a list of the PDB IDs, results of the PCA and values of the introduced features in the structures. cMD: Input parameters, topologies and starting coordinates of the five classical MD simulation that are based on different PDB structures, resulting trajectories, projection on X-ray PCA, RMSD values and values of the introduced features during the simulations. TMD: Input parameters, topologies and starting coordinates of the Targeted MD simulations, resulting trajectories, projection on X-ray PCA, RMSD values and values of the introduced features during the simulations. Seeded-Sims: Input parameters, topologies and starting coordinates of classical MD simulations that are started from cluster representatives of the TMD simulations and resulting trajectories. MSM: Values of the introduced features of the trajectories started from the TMD seeds, results of the TICA and of the denity-based clustering, representative structures of the states E, I1, I2 and E* and distribution of the introduced features in these states. A more detailed description of the included files can be found in the README files in each folder. Additional information about software versions can also be found there.