Molecular docking
Molecular modeling studies were performed using Discovery Studio Programs (2018, Accelrys) and figures were generated using PyMOL programs. The 3D coordinates of human SphK1 complexed with ADP were obtained from the protein data bank for docking studies (PDB entry 3VZD). 3VZD represents a tetrameric crystal structure of SphK1 that includes six monomers (A-F). Monomer C was chosen for the simulations based on its displacement property. ADP, which binds between the N-terminal and C-terminal domains, was removed from the complex. Preparation of the protein was performed with the Prepare Protein protocol and a binding site was created using the Define and Edit Binding Site protocol (default parameters were used). Energy minimization of ligands was performed by the Clean Geometry module in Discovery Studio, and conformations were generated using the Generate Conformations…
