| Code | Name | Deposits | Targets | Ligand Type |
|---|---|---|---|---|
| LLP | PYRIDOXAL-5''-PHOSPHATE | 9 | 5 | modified residue |
| UNX | Unknown atom | 9 | 3 | crystallization |
| KAN | 8 | 3 | biological | |
| ADP | 8 | 8 | biological | |
| NA | 8 | 3 | biological | |
| SO4 | sulfate | 8 | 8 | biological |
| SAH | 7 | 3 | biological | |
| NAP | 7 | 7 | biological | |
| SIN | succinic acid | 7 | 7 | crystallization |
| TAR | tartrate | 7 | 7 | crystallization |
| SUC | sucrose | 7 | 7 | crystallization |
| MLA | 7 | 4 | crystallization | |
| EPE | 7 | 6 | other | |
| DMS | 6 | 4 | crystallization | |
| NDP | Nicotinamide adenine dinucleotide phosphate | 6 | 6 | biological |
| CSX | 6 | 6 | modified residue | |
| GDP | 6 | 6 | biological | |
| BDF | beta-d-fructopyranose | 6 | 4 | crystallization |
| MES | MES | 6 | 6 | other |
| MLT | 6 | 5 | crystallization |