Molecular Dynamics Simulation of PKD2 PH–Catalytic Domain Interface in Complex with Allosteric Inhibitor CC2-55

This dataset contains molecular dynamics (MD) simulation data of the human Protein Kinase D2 (PKD2) in its autoinhibited conformation, focusing on the interaction between the pleckstrin homology (PH) domain and the catalytic (CAT) domain in the presence of the allosteric inhibitor CC2-55. The initial structural model was constructed based on a hybrid approach combining homology modelling of the catalytic domain and an experimentally determined PH domain structure, assembled into a closed, autoinhibited conformation. The inhibitor CC2-55 was positioned at the PH–CAT interface based on structure-based docking and pharmacophore-guided screening. All-atom MD simulations were performed to investigate the stability of the PH–CAT interface and the effect of CC2-55 binding on the conformational dynamics of PKD2. The simulations were carried out in explicit solvent conditions with periodic boundary conditions, following standard equilibration and production protocols. This dataset includes representative trajectories, topology and parameter files, and selected snapshots illustrating key interaction states. The data support the conclusions presented in the associated manuscript regarding ATP-independent, allosteric stabilization of the PKD2 autoinhibited conformation.