Validation of cycle conformation in small molecules
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| Year of publication | 2022 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | The structural data of biomacromolecules are an essential input for various fields of science. The Protein Data Bank (PDB) contains more than 190,000 experimentally determined structures. The PDB database is one of the most widely used sources of three-dimensional structural data of macromolecules and small molecules - ligands. Although each molecular structure is validated before the deposition, some structures may contain minor or major errors. With the growth of the number of determined structures, it is necessary to pay more attention to data quality. A large number of biomacromolecule and ligand structure quality criteria are established. However, some of them are still not included in validation reports, such as validation of conformation of the cycle. Incorrect determination of the cycle conformation in the ligands may impact the geometric property of a macromolecule or molecular fragments in the surrounding area. We focused on the validation of basic cycles such as cyclopentane, cyclohexane and benzene. Firstly, we compare the experimentally determined conformation of the ligand from the PDB database with templates of ideal conformation of cycles. In the next step, we analysed the electron density coverage of each atom in the cycle. We analysed the occurrence of the untypical conformation of ligands. Subsequently, we examined the reasoning for selecting the energetically unfavoured conformations. |
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