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

Darius Lingė, Marius Gedgaudas, Andrius Merkys, Vytautas Petrauskas, Antanas Vaitkus, Algirdas Grybauskas, Vaida Paketurytė, Asta Zubrienė, Audrius Zakšauskas, Aurelija Mickevičiūtė, Joana Smirnovienė, Lina Baranauskienė, Edita Crossed D sign apkauskaitė, Virginija Dudutienė, Ernestas Urniežius, Aleksandras Konovalovas, Egidijus Kazlauskas, Kirill Shubin, Helgi B. Schiöth, Wen Yih ChenJohn E. Ladbury, Saulius Gražulis, Daumantas Matulis

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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/

Original languageEnglish
Article numberbaad040
JournalDatabase : the journal of biological databases and curation
Volume2023
DOIs
StatePublished - 2023

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