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Document Figure 3 The sequence alignment of MMPs with the catalytic domain region highlighted. The residues that line the subtrate pockets are marked: S3 (3), S2 (2), S1 (1), S1 (*), S2' (@), and S3' (#). The highlighted catalytic domain alignment was dominated by the structural alignment of the determined structures of HFC, HNC, and matrilysin. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_175.html (2 of 2) [4/5/2004 5:03:13 PM]
Document Page 176 0.43 Å) as the catalytic-domain structure of HFC. This demonstrates that the absence or presence of the hemopexin domain does not affect the overall structure of the catalytic domain. The sequence homology of the catalytic domains of the collagenases is 62%. This can be extended to the other members of the MMP family as seen in Figure 3. An understanding of the structural features of the target enzyme is essential for structure-based drug design. In this example we will be looking at inhibiting MMPs by binding to the active site. The numbering system used throughout this chapter will be in regard to the HFC sequence used in 1hfc.pdb. III. Surface Features The surface features of matrilysin, fibroblast collagenase, and neutrophil collagenase are all similar (Figure 4). The active-site groove can be plainly seen on the surface: two main pockets punctuated by the active-site zinc. Modeling Figure 4 The accessible surfaces of HFC (a), HNC (b), and matrilysin (c) are shown with a bound P'-side hydroxamate inhibitor. http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_176.html (1 of 2) [4/5/2004 5:03:26 PM]
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