The detailed structures of microsomal prostaglandin E synthase-1 (mPGES-1) binding with inhibitors have been studied, for the first time, by using a newly developed computational three-dimensional (3D) structural model of mPGES-1 along with a 3D-quantitative structure--activity relationship (3D-QSAR) analysis. The obtained satisfactory binding structures and 3D-QSAR models strongly suggest that the 3D structural model of mPGES-1 is reasonable for study of mPGES-1 binding with inhibitors and for future design of novel mPGES-1 inhibitors.