Logo scPDB


An Annotated Database of Druggable Binding Sites from the Protein DataBank

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To assist structure-based approaches in drug design, we have processed the PDB to identify binding sites suitable for the docking of a drug-like ligand and we have so created a database called sc-PDB.

The sc-PDB database provides separated MOL2 files for the ligand, its binding site and the corresponding protein chain(s). Ions and cofactors at the vicinity of the ligand are included in the protein.
More details about the sc-PDB scope, its content and its evolution during the 2004-2009 period are provided in a pdf document.

Web site specifications :
The current release v.2017 was made using the frozen PDB data on 2016-11.
It contains 16034 entries, which correspond to 4782 different proteins and 6326 different ligands.
The full database totals 3.8 GB compressed.
Manual corrections are occasionally applied to the database.