4.3. Molecular Docking

The crystal structure of CDK4 in complex with flavopiridol that has been resulted from superimposition of (CDK2 + Flavopiridol) (pdb code = 2W9Z) and CDK4 (pdb code = 6GUB). The resulted (CDK4 + Flavopiridol) model was used for molecular docking and the protein was prepared prior to the docking process by MOE 2016.08 in which minimization were done. Hydrogen atoms were added, and the docking site was identified and selected. All compounds were built and saved as (moe). Rigid receptor was used as a docking protocol. Both receptor and solvent were kept as a “receptor”. Triangle matcher was used as a placement method. Two rescoring were computed, rescoring 1 was selected as London dG. Rescoring 2 was selected as affinity. Force field was used as a refinement. All coordinates were derived from pdb and all interactions were observed with the conserved residues. The docking protocol used the triangle method as a placement method with timeout of 300 s, and number of return poses as 1000. London dG was used as a rescoring method. Force field was used as a refinement method by applying MMFF94x.