Invesigating the rare conformation of small rings in ligands
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| Year of publication | 2023 |
| Type | Appeared in Conference without Proceedings |
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| Description | Various aspects of biomacromolecular quality are validated through established metrics, including evaluating protein backbone torsion angles or the number of clashes. In parallel, validating small molecules alongside biomacromolecules in structure models is increasingly important for drug design and pharmaceutical research. However, the field of ligand validation is still evolving, and not all aspects of ligand quality are examined. This study aims to investigate whether rings, which are critical components of ligands, can only exist in stable conformations within protein structures or if they can adopt energetically unfavourable conformations under specific conditions, such as the interaction with the binding site of the macromolecule. The focus is on commonly occurring five and six-membered carbon rings, analysing their occurrences and conformations in the PDB. We used data obtained via X-ray crystallography, the most used method for determining the structures of macromolecular complexes, as we can validate the model based on the electron density coverage. Subsequently, we investigated the relationship between structure and function in energetically unfavourable ring conformations. |
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