Abstract
BackgroundBiological chemistry is very stereospecific. Nonetheless, the diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distinguish them from each other due to the lack of standardization. This issue has largely not been addressed by the protein structure community.ResultsOf 472 diastereotopic atom pairs studied from the PDB, 118 were found to have names that are not uniquely assigned. Among the molecules identified with these inconsistencies were many cofactors of enzymatic processes such as mononucleotides (e.g. ADP, ATP, GTP), dinucleotide cofactors (e.g. FAD, NAD), and coenzyme A. There were no overall trends in naming conventions, though ligand-specific trends were prominent.ConclusionThe lack of standardized naming conventions for diastereotopic atoms of small molecules has left the ad hoc names assigned to many of these atoms non-unique, which may create problems in data-mining of the PDB. We suggest a naming convention to resolve this issue. The in-house software used in this study is available upon request.A version of the software used for the analyses described in this paper is available at our web site: .
Highlights
Note the differences in names for the pro-R and pro-S atoms. Both molecules of nicotinamideadenine dinucleotide (NAD) shown are from an alcohol dehydrogenase structure [Protein Data Bank (PDB):2OHX][16]
That was eleven years ago and only involved a study of 32 protein structures. This was long before the recent remediation project of the PDB [18]. This project has done well to bring molecular and atomic naming conventions for PDB files into conformity with standards established by the International Union of Pure and Applied Chemistry (IUPAC) and the International Union of Biochemistry and Molecular Biology (IUBMB)
Atoms were considered to be covalently bonded if the distance between their centers was less than the sum of their covalent radii plus a cushion of 0.4 Å, following the custom of the Cambridge Structural Database (CSD) [19]
Summary
The diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distinguish them from each other due to the lack of standardization. This issue has largely not been addressed by the protein structure community. Often accompanying the macromolecules deposited in the Protein Data Bank (PDB) [1] are smaller molecules of biological importance. Some of these are energy-carrying cofactors, such as ATP, coenzyme A, and nicotinamideadenine dinucleotide (NAD). Two of these groups are identical, the center atom is prochiral, meaning that (page number not for citation purposes)
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