Table 1. Downloadable content of sc-PDB.
| filename | Number of entries in file | Data description | Data type |
|---|---|---|---|
| protein.mol2 | one or list of PDB ID matching search criteria | All-atom description of sc-PDB protein(s) | Atomic data |
| ligand.mol2 | one or list of PDB ID matching search criteria | All-atom description of sc-PDB ligand | Atomic data |
| site.mol2 | one or list of PDB ID matching search criteria | All-atom description of sc-PDB ligand binding site | Atomic data |
| cavity6.mol2 | one or list of PDB ID matching search criteria | The cavity is the negative image of the binding site, described by regularly spaced points colored according to pharmacophoric properties of the site atoms | Atomic data |
| ints_M.mol2 | one or list of PDB ID matching search criteria | Non-bonded interactions between sc-PDB ligand and its binding site | Atomic data |
| Each interaction is characterized by three points, placed respectively on the protein atom in interaction, the ligand atom in interaction and at the center of the segment defined by these two points | |||
| ifp.txt | one or list of PDB ID matching search criteria | Non-bonded interactions between sc-PDB ligand and its binding site | Binary string |
| For each residue in site is marked the presence or absence of interaction with ligand (hydrophobic contact, aromatic bond, H-bond, ionic bond, metal-ion bond) | |||
| C-clusterID.tar.gz | Clusters of binding sites | The archive classifies all the sc-PDB entries of a UNIPROT protein. It is organized into directories, one for each cluster of sites. Each cluster contains protein.mol2, site.mol2 and ligand.mol2 files of all individual PDB entries, which have been 3D-aligned to the site at cluster center | Atomic data |
| Alignment.tar.gz | Pair of PDB ID, 3D-aligned for optimizing site similarity (1) or binding mode similarity (2) | The archive describes the protein, site, ligand and cavity (1) or non-bonded interaction (2) files for the reference entry (original coordinates) and the compared entry (fitted coordinates) | Atomic data |
| scPDB_results | list of entries matching search criteria | Annotation and 2D structure of ligands in csv, xlsx or sdf formats | Text |
| PDBID_distribution.tsv | list of entries similar to query site (1) or query binding mode (2) | Similarity scores | Text |
All charts and pictures of sc-PDB website are downloadable in png format. The complete database is downloadable as a compressed archive from the database homepage.