Carboxypeptidase G(2) (CPG(2)) is a zinc-metalloenzyme employed in a range of cancer chemotherapy strategies by activating selectively nontoxic prodrugs into cytotoxic drugs in tumor as well as in the treatment of intoxication caused by high-doses of the anticancer drug methotrexate (MTX). CPG(2) catalyzes the hydrolytic cleavage of C-terminal of glutamate moiety from folic acid and analogues. Regardless of its extensive application, its mechanism of catalysis has not yet been determined and, so far, no co-crystallized complex has been published. So, in this study, molecular docking and a short molecular dynamics (MD) simulation sampling scheme, as a function of temperature, were performed to investigate a possible binding mode for MTX, a recognized substrate of CPG(2). The findings suggested that MTX interacts possibly in quite specific points of the CPG(2) active site, which are probably responsible for the molecular recognition and cleavage procedures. The MTX substrate fits well in the catalytic site by accommodating the pteridine moiety in an adjacent pocket to the active site whereas a glutamate moiety is pointed toward the protein surface. Additionally, a glutamate residue can interact with a crystallization water molecule in the active site, supporting its activation as a nucleophilic group.