sc-PDB: a 3D-database of ligandable binding sites--10 years on.
Bottom Line: The sc-PDB database was publicly launched in 2004 with the aim of providing structure files suitable for computational approaches to drug design, such as docking.During the last 10 years we have improved and standardized the processes for (i) identifying binding sites, (ii) correcting structures, (iii) annotating protein function and ligand properties and (iv) characterizing their binding mode.The new website puts emphasis in pictorial analysis of data.
Affiliation: Laboratoire d'innovation thérapeutique, Medalis Drug Discovery Center, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, France.Show MeSH
Mentions: The sc-PDB database now enables the identification of similar 3D pattern in distinct complexes; the all-against-all comparison of sc-PDB complexes was computed using the program Grim (26). The sc-PDB website allows to query the matrix of scores for any given sc-PDB ligand/protein binding mode. It displays the distribution of scores and lists the entries whose similarity score is higher than the threshold selected on the distribution (default value is 0.65). For example, the binding mode of phosphomethylphosphonic acid-guanylate ester to E. coli adenylosuccinate synthetase (PDB ID: 1HOP, HET: CGP) shares significant similarity with 25 complexes in sc-PDB, representing 19 different proteins bound to GDP, GTP or close analogs. The two top scorers are respectively a homologous protein in wheat (PDB ID: 1DJ3) and the functionally unrelated signal recognition particle protein (PDB ID: 1RJ9, Figure 3).
Affiliation: Laboratoire d'innovation thérapeutique, Medalis Drug Discovery Center, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, France.