Drugs
The PDBe RelLig pipeline identifies drug-like ligands in the PDB by utilizing drug-target annotations found in the ligand CIF files available from the PDBe FTP. These CIF files are updated weekly and include drug-target data sourced from the DrugBank database.
Annotation process
The PDBe RelLig pipeline parses the input PDB ligand CIF file to retrieve any available drug-target annotations. It then uses the PDBe API to gather all proteins interacting with the ligand. If any of these proteins are pharmacologically active targets, the ligand is annotated as drug-like.
Example
PDBe RelLig pipeline identifies STI (Imatinib) as drug-like molecule with drug-target Tyrosine-protein kinase ABL1 and write the output with ligand interacting proteins from the PDB
| pdb_id | auth_asym_id | struct_asym_id | uniprot_id | name | organism |
|---|---|---|---|---|---|
| 7n9g | A | A | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 3pyy | B | B | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 6npu | B | B | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 6npe | A | A | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 2hyy | A | A | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 6npu | A | A | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 6npv | B | B | P00519 | Tyrosine-protein kinase ABL1 | Humans |
| 6npe | B | B | P00519 | Tyrosine-protein kinase ABL1 | Humans |