We have mapped the substrates deposited in MEROPS onto the structural database PDB and obtained a subset of protein substrates with experimentally solved 3D structures. The subset of these substrate PDB structures for the major proteases families are listed in the following.

- Protease A01.001: Pepsin A (292 entries)
- Protease A01.009: Cathepsin D (122 entries)
- Protease A01.010: Cathepsin E (113 entries)
- Protease A01.012: Rhizopuspepsin (192 entries)
- Protease A01.016: Aspergillopepsin I (128 entries)
- Protease A01.053: Necepsin-1 (108 entries)
- Protease A02.001: HIV-1 retropepsin (125 entries)
- Protease C01.032: Cathepsin L (157 entries)
- Protease C01.033: Cathepsin L1 ({Fasciola} sp.) (168 entries)
- Protease C01.034: Cathepsin S (124 entries)
- Protease C01.046: Falcipain-2 (118 entries)
- Protease C01.060: Cathepsin B (139 entries)
- Protease C01.063: Falcipain-3 (96 entries)
- Protease C14.001: Caspase-1 (6 entries)
- Protease C14.003: Caspase-3 (51 entries)
- Protease C14.004: Caspase-7 (8 entries)
- Protease C14.005: Caspase-6 (39 entries)
- Protease C14.006: Caspase-2 (1 entries)
- Protease C14.009: Caspase-8 (1 entries)
- Protease C14.015: Caspase (insect 1) (2 entries)
- Protease M10.001: Matrix metallopeptidase-1 (15 entries)
- Protease M10.002: Matrix metallopeptidase-8 (12 entries)
- Protease M10.003: Matrix metallopeptidase-2 (458 entries)
- Protease M10.004: Matrix metallopeptidase-9 (62 entries)
- Protease M10.005: Matrix metallopeptidase-3 (22 entries)
- Protease M10.007: Matrix metallopeptidase-11 (4 entries)
- Protease M10.008: Matrix metallopeptidase-7 (12 entries)
- Protease M10.009: Matrix metallopeptidase-12 (16 entries)
- Protease M10.013: Matrix metallopeptidase-13 (7 entries)
- Protease M10.014: Membrane-type matrix metallopeptidase-1 (17 entries)
- Protease M10.016: Membrane-type matrix metallopeptidase-3 (1 entries)
- Protease M10.018: Matrix metallopeptidase-18 (1 entries)
- Protease M10.021: Matrix metallopeptidase-19 (5 entries)
- Protease M10.024: Membrane-type matrix metallopeptidase-6 (15 entries)
- Protease M10.029: Matrix metallopeptidase-26 (3 entries)
- Protease M10.051: Serralysin (1 entries)
- Protease M10.057: Mirabilysin (9 entries)
- Protease M12.001: Astacin (62 entries)
- Protease M12.002: Meprin alpha subunit (92 entries)
- Protease M12.004: Meprin beta subunit (94 entries)
- Protease M12.033: LAST_MAM peptidase (136 entries)
- Protease M16.002: Insulysin (25 entries)
- Protease S01.001: Chymotrypsin A (cattle-type) (256 entries)
- Protease S01.010: Granzyme B ({Homo sapiens}-type) (74 entries)
- Protease S01.131: Elastase-2 (117 entries)
- Protease S01.133: Cathepsin G (71 entries)
- Protease S01.269: Glutamyl peptidase I (302 entries)
- Protease S01.280: Lysyl peptidase (bacteria) (58 entries)