A drug-metabolizing enzyme prediction apparatus acquires compound structure information, identifies binding site information and molecular species information based on a binding-site identifying condition, specifies a pinching point that is an atom binding at least between a reactive site and a binding site, acquires pinching point information on the specified pinching point and reactive site information on the reactive site bound to the pinching point, and identifies the acquired reactive site information based on a reactive-site identifying condition and the acquired pinching point information based on a pinching-point identifying condition.