| Code | Name | Deposits | Targets | Ligand Type |
|---|---|---|---|---|
| DA | unknown | 3 | 2 | biological |
| DAL | 3 | 3 | biological | |
| DAL | 1 | 1 | crystallization | |
| DAU | 2'deoxy-thymidine-5'-diphospho-alpha-d-glucose | 1 | 1 | biological |
| DC | unknown | 3 | 2 | biological |
| DCF | 2'-deoxycoformycin | 1 | 1 | crystallization |
| DEA | d-eritadenine | 1 | 1 | biological |
| DG | unknown | 3 | 2 | biological |
| DGL | d-glutamic acid | 1 | 1 | biological |
| DKA | 1 | 1 | biological | |
| DME | decamethonium ion | 1 | 1 | crystallization |
| DMS | 6 | 4 | crystallization | |
| DRG | 2 | 2 | crystallization | |
| DSZ | 5'-o-(l-alpha-aspartylsulfamoyl)adenosine | 2 | 2 | biological |
| DT | unknown | 3 | 2 | biological |
| DTT | 2,3-dihydroxy-1,4-dithiobutane | 1 | 1 | crystallization |
| EDO | ethylene diol | 2 | 2 | biological |
| EDO | ethylene diol | 187 | 129 | crystallization |
| EDO | ethylene diol | 1 | 1 | modified residue |
| EDO | ethylene diol | 20 | 18 | other |