Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, an efficient mechanism for identifying possible protein-ligand interactions based on analysis of protein tertiary substructures is proposed. In one experiment reported in this papert, the proposed prediction mechanism has been exploited to obtain some clues about a hypothesis that the biochemists have been speculating. The main distinction in the design of the prediction mechanism is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in a cave of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the α-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a 3-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.11 to 9.79 times.