How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)
G. Michael Blackburn, Jacqueline Cherfils, Gerard P. Moss, et al. Pure and Applied Chemistry, 2017Volume 89, Issue 5, pp. 653-675
Procedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g.,biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to “best practice” in the PDB, especially to the atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates, but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly.
©2018 IUPAC & De Gruyter. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. For more information, please visit: http://creativecommons.org/licenses/by-nc-nd/4.0/
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Articles in the same Issue
- Masthead - Full issue pdf
- President's Column
- Keeping Momentum up and Looking Forward
- Features
- Bonding the World with Chemistry
- Australia and IUPAC
- 150 Years of Chemical Society in Germany
- Green Chemistry for Sustainable Development
- IUPAC Wire
- Members of ICSU and ISSC Vote To Merge
- 2018 IUPAC-ThalesNano Prize in Flow Chemistry and Microfluidics – Call For Nominations
- Stamps International
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- InChI’ng forward: Community Engagement in IUPAC’s Digital Chemical identifier
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- How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016)
- A critical review of the proposed definitions of fundamental chemical quantities and their impact on chemical communities (IUPAC Technical Report)
- Preferred names of constitutional units for use in structure-based names of polymers (IUPAC Recommendations 2016)
- Calibration, standardization, and quantitative analysis of multidimensional fluorescence (MDF) measurements on complex mixtures (IUPAC Technical Report)
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- Innovative new technologies for chemical security, safety, and health
- Colloquium Spectroscopicum Internationale XL
- Advanced Polymers via Macromolecular Engineering
- Development of chemistry within planetary boundaries
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- Mark Your Calendar
