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

Desaphy J, Bret G, Rognan D, Kellenberger E - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire d'innovation thérapeutique, Medalis Drug Discovery Center, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, France.

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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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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).

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).


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

Desaphy J, Bret G, Rognan D, Kellenberger E - Nucleic Acids Res. (2014)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384012&req=5

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).
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).

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.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire d'innovation thérapeutique, Medalis Drug Discovery Center, UMR7200 CNRS-Université de Strasbourg, F-67400 Illkirch, France.

Show MeSH