Calcium-Dependent Protein Kinase 5 (CDPK5) protein is one of the family members of a calcium-dependent protein kinase that is found in plants and some species of protozoa which includes Plasmodium falciparum (Pf), the pathogen responsible for malaria. CDPKs regulate many biological processes in Apicomplexans such as Plasmodium, Toxoplasma or Cryptosporidium. The study addresses the similarity in sequences and evolutionary relationship of CDPK5 across Apicomplexans. Further, the three-dimensional structural conformation of PfCDPK5 is generated through homology modeling. Molecular dynamics simulation of the homology model for a time interval of 40 ns resulted in a stable conformation of the PfCDPK5 protein. Inhibitor identification was carried out from computational screening of known anti-malarial compounds. The reliability of the binding mode for the best inhibitor compound MMV687246 was validated through a complex molecular dynamics study. This findings advocates that MMV687246 from Pathogen Box as the best inhibitor against PfCDPK5 protein and can be considered for experimental validation study in future.