title: Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.
abstract: Protein-protein interactions (PPIs) play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP) complexes, and 161 protein-ligand (PL) complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.
authors.affiliation: Center for Bioinformatics, Saarland University, Building E2 1, P.O. Box 151150, 66041, Saarbruecken, Germany; Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), 42300 Puncak Alam, Selangor, Malaysia.
authors.forename: Ruzianisra
authors.initials: R
authors.lastname: Mohamed
authors.affiliation: Center for Bioinformatics, Saarland University, Building E2 1, P.O. Box 151150, 66041, Saarbruecken, Germany.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Degac
authors.affiliation: Center for Bioinformatics, Saarland University, Building E2 1, P.O. Box 151150, 66041, Saarbruecken, Germany.
authors.forename: Volkhard
authors.initials: V
authors.lastname: Helms
mesh_terms: D000596:Amino Acids; D001665:Binding Sites / Q000235:genetics / Q000502:physiology; D030562:Databases, Protein; D006801:Humans; D008024:Ligands; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D054730:Protein Interaction Domains and Motifs / Q000235:genetics / Q000502:physiology
chemical_list: D000596:Amino Acids; D008024:Ligands