Abstract
BackgroundCurrently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function.DescriptionHere we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients.ConclusionSuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.
Highlights
The Protein Data Bank (PDB) contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds
Description: Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types
SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures
Summary
The database presented here supplements the set of existing resources of information about small molecules bound to PDB structures. The FULL info button delivers detailed information about the selected PDB ligand like molecular formula, atom numbers and occurrence in the PDB. After clicking the DRUGS button, a two-dimensional similarity search among the drugs in the SuperDrug database [16] is performed. A following spatial superposition of the best hits reveals a further COX-2 inhibitor, namely valdecoxib, (RMSD 0.26Å and 21 of 22 atoms superposed) as very similar to celecoxib. The three-dimensional comparison here proves to be very important to reveal molecular similarities in addition to topological comparison (as shown in the example in the section Utility), which is confirmed by the fact that valdecoxib was categorised as toxic [19] and sales of this drug were suspended recently [20].
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