Comparison of Two Independent Crystal Structures of Human Dihydrofolate Reductase Ternary Complexes Reduced with Nicotinamide Adenine Dinucleotide Phosphate and the Very Tight-Binding Inhibitor PT523,

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Abstract
Structural data for two independent crystal forms (monoclinic, C2, and orthorhombic, P212121) of the ternary complex of the potent antitumor agent PT523 [Nα-(4-amino-4-deoxypteroyl)-Nδ-hemiphthaloyl-l-ornithine], reduced nicotinamide adenine dinucleotide phosphate (NADPH), and recombinant human dihydrofolate reductase (hDHFR) reveals multiple binding orientations for the hemiphthaloyl group of the inhibitor. Analysis of these data shows that PT523 binds with its pteridine ring in the same orientation observed for methotrexate (MTX) analogues. However, in each structure, the hemiphthaloyl ring occupies three alternate conformations. In the C2 lattice, the phthaloyl moiety binds in two extended conformations, A and C, with each conformer having a 180° flip of the o-carboxylate group, and a third, lower occupancy conformer B, with the phthaloyl group folded within contact of the active-site pocket. In the orthorhombic lattice, PT523 also has three conformers for the phthaloyl group; however, these differ from those observed in the monoclinic lattice. Two major conformers, A and C, are displaced on either side of the extended position observed in the C2 lattice, one near the folded B conformer of the C2 lattice and the other extended. These conformers form tighter intermolecular contacts than those in the C2 lattice. Conformer B is folded back away from the active site in a unique position. There are also significant differences in the conformation of the adenine−ribose moiety of NADPH in both complexes that differ from that observed for other inhibitor−NADPH−hDHFR ternary complexes. These data suggest that the added intermolecular contacts made by the hemiphthaloyl group of PT523 contribute to its tighter binding to hDHFR than MTX, which does not extend as far from the active site and cannot make these contacts. These crystallographic observations of multiple conformations for the hemiphthaloyl group are in general agreement with solution NMR data for the binding of PT523 to hDHFR [Johnson et al. (1997) Biochemistry 36, 4399−4411], which show that the hemiphthaloyl group may adopt more than one conformation. However, the crystallographic data reveal more discretely occupied positions than can be interpreted from the solution data. These results suggest that crystal packing interactions may influence their stability.