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. 2015 Jan;43(Database issue):D399-404.
doi: 10.1093/nar/gku928. Epub 2014 Oct 9.

sc-PDB: a 3D-database of ligandable binding sites--10 years on

Jérémy Desaphy  1 , Guillaume Bret  1 , Didier Rognan  1 , Esther Kellenberger  2
Affiliations

sc-PDB: a 3D-database of ligandable binding sites--10 years on

Jérémy Desaphy et al. Nucleic Acids Res. 2015 Jan.

Abstract

The sc-PDB database (available at http://bioinfo-pharma.u-strasbg.fr/scPDB/) is a comprehensive and up-to-date selection of ligandable binding sites of the Protein Data Bank. Sites are defined from complexes between a protein and a pharmacological ligand. The database provides the all-atom description of the protein, its ligand, their binding site and their binding mode. Currently, the sc-PDB archive registers 9283 binding sites from 3678 unique proteins and 5608 unique ligands. 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. This paper presents the latest enhancements in the database, specifically pertaining to the representation of molecular interaction and to the similarity between ligand/protein binding patterns. The new website puts emphasis in pictorial analysis of data.

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Figures

Figure 1.
Figure 1.
The general flow chart from PDB to sc-PDB.
Figure 2.
Figure 2.
Crystallographic water molecules in sc-PDB binding sites.
Figure 3.
Figure 3.
Search the sc-PDB for similar binding modes. Screenshots display the distribution of values for a given query binding mode (top left), the ranked list of similar entries (bottom left) and the 3D alignment of a selected hit with the query complex (top right). The closer view (bottom right) better shows aligned interaction points. The 3D structure of the query is colored in yellow (PDB ID: 1hop, HET: GCP), the selected hit in green (PDB ID: 1rj9, HET: GCP). Interaction pseudo-atoms are colored by interaction type (green, hydrophobic; blue, H-bond with ligand acceptor; red, H-bond with ligand donor; brown, metal chelation).
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