PLBD: protein–ligand binding database of thermodynamic and kinetic intrinsic parameters

• Published in: Database : the journal of biological databases and curation 2023-06, Vol.2023
• Main Authors: Lingė, Darius, Gedgaudas, Marius, Merkys, Andrius, Petrauskas, Vytautas, Vaitkus, Antanas, Grybauskas, Algirdas, Paketurytė, Vaida, Zubrienė, Asta, Zakšauskas, Audrius, Mickevičiūtė, Aurelija, Smirnovienė, Joana, Baranauskienė, Lina, Čapkauskaitė, Edita, Dudutienė, Virginija, Urniežius, Ernestas, Konovalovas, Aleksandras, Kazlauskas, Egidijus, Shubin, Kirill, Schiöth, Helgi B, Chen, Wen-Yih, Ladbury, John E, Gražulis, Saulius, Matulis, Daumantas
• Format: Article
• Language: English
• Subjects: Original
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/baad040

Abstract We introduce a protein–ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein–ligand crystal structures, enabling structure–thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein–ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein–ligand recognition and could be integrated into small molecule drug design. Database URL https://plbd.org/