10.1021/jm0703385.s001 Christine L. Gee Christine L. Gee Nyssa Drinkwater Nyssa Drinkwater Joel D. A. Tyndall Joel D. A. Tyndall Gary L. Grunewald Gary L. Grunewald Qian Wu Qian Wu Michael J. McLeish Michael J. McLeish Jennifer L. Martin Jennifer L. Martin Enzyme Adaptation to Inhibitor Binding:  A Cryptic Binding Site in Phenylethanolamine <i>N</i>-Methyltransferase American Chemical Society 2007 side chain conformations crystal structure site size 140 Å3 Enzyme Adaptation Cryptic Binding Site site increases PNMT inhibitor design body helix motions SK enzyme complexed binding site protein flexibility 2007-10-04 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/Enzyme_Adaptation_to_Inhibitor_Binding_A_Cryptic_Binding_Site_in_Phenylethanolamine_i_N_i_Methyltransferase/2982172 Shape complementarity is a fundamental principle of inhibitor design. Here we show that an enzyme for which the crystal structure has been determined (phenylethanolamine <i>N</i>-methyltransferase, PNMT) conceals a cryptic binding site. This site is revealed upon binding of inhibitors that are double the size of the physiological substrate. These large inhibitors are not predicted to bind in that they protrude through the accessible surface calculated from a PNMT/7-aminosulfonyl-1,2,3,4-tetrahydroisoquinoline (SK&F 29661) crystal structure, yet they are potent inhibitors of PNMT. We determined structures of the enzyme complexed with large inhibitors and found that the volume of the active site increases by 140 Å<sup>3</sup> upon binding. Changes in active site size and shape are brought about by unfavorable side chain conformations and rigid body helix motions. The energetic cost is modest, estimated at 2−3 kcal/mol from mutational analyses. Our findings further underline the importance of protein flexibility in structure-based inhibitor design studies.