Reactants
The PDBe RelLig pipeline identifies reactant-like ligands in the PDB by comparing their 2D structural similarity to reactants in the Rhea database, a curated resource that uses the ChEBI ontology to describe reaction participants and their structures.
Annotation process
The pipeline analyzes input PDB ligands, then retrieves the proteins interacting with these ligands using the PDBe API. For each protein, the corresponding catalysis reactions and reaction participants are obtained through the Uniprot SPARQL and Rhea SPARQL endpoints, respectively. The PARITY method is used to compare the structural similarity of PDB ligands to reaction participants represented by the ChEBI ontology. Ligands with a minimum similarity score of 0.7 are classified as reactant-like, ensuring accurate identification of biologically relevant reactants (either the substrate or product of the reaction).
Example
PDBe RelLig pipeline identifies 1CP (COPROPORPHYRINOGEN I) as reactant-like molecule and writes the output with interacting proteins from the PDB and similarities to reaction participants present in the reactions catalysed the protein.
| pdb_id | auth_asym_id | struct_asym_id | uniprot_id | rhea_id | chebi_id | similarity |
|---|---|---|---|---|---|---|
| 1r3q | A | A | P06132 | 19865 | 57308 | 0.714 |
| 1r3q | A | A | P06132 | 31239 | 62626 | 0.8 |
| 1r3q | A | A | P06132 | 31239 | 62631 | 1.0 |
| 1r3s | A | A | P06132 | 19865 | 57308 | 0.714 |
| 1r3s | A | A | P06132 | 31239 | 62626 | 0.8 |
| 1r3s | A | A | P06132 | 31239 | 62631 | 1.0 |
| 1r3v | A | A | P06132 | 19865 | 57308 | 0.714 |
| 1r3v | A | A | P06132 | 31239 | 62626 | 0.8 |
| 1r3v | A | A | P06132 | 31239 | 62631 | 1.0 |