The positions of the substrates (ATP and ribose 5 phosphate) of phosphoribosylpyrophosphate synthetase from Thermus thermophilus were determined by molecular dynamics simulations. The simulation brought the system to an equilibrium state, with the binding poses of the ligands in the active site being stable. Based on the results of simulation of the complex, the environment of the substrates was analyzed and the amino-acid residues of the enzyme that form polar interactions with the substrates were identified. Candidate sites for mutagenesis, which can be mutated in order to broaden the substrate specificity toward ribose 5-phosphate, are proposed.