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Comprehensive Methods for Searching Sugar Derivatives: An Overview

This guide outlines effective searching methods for sugar derivatives, specifically focusing on the D-Series. It details parameters for identifying 5 or 6-membered rings containing oxygen and crucial hydroxyl groups. It covers linear chains with carbonyl groups, various disaccharides like sucrose and lactose, and includes the use of Marvinsketch for effective chemical component dictionary searches. It also compares search results from the PDBe and RCSB databases, discussing discrepancies and the inclusion of straight-chain carbohydrates and sugar alcohols.

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Comprehensive Methods for Searching Sugar Derivatives: An Overview

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  1. Sugar Searching Methods Ya-Min Chi, Sarah Goodman, Aileen Zaydel

  2. Parameters for searching • 5 or 6 membered ring with an oxygen in position 5 or 6, respectively • Rings must have a hydroxyl group at the carbon next to the oxygen (C1) • Linear chain must contain a carbonyl group (not a priority)

  3. Basic Searches In The Chemical Component Dictionary

  4. Derivatives of Sugars from the D-Series -aric acid -itol -ose -onic acid -uronic acid

  5. Prefixes and Suffixes Disaccharides Other • Sucrose • Lactose • Maltose • Trehalose • Cellobiose • Neuraminic acid • Sialic acid • Amylose • ose • oside • furan • pyran • amine • N-acetyl • onolactone • trihydroxy/hydroxymethyl

  6. Using Marvinsketch

  7. Results

  8. General sugars • Pyranoside • Pyranosyl • Pyranose • Furanoside • Furanosyl • Furanose • Ribulo • Xylulo • Biose • Triose • Idose • Trehalose

  9. Thiosugars Azasugars • C-S-C (6 membered and 5 membered) • THIO/fragment • C-N-C • Isofagomine • Neuromycin

  10. PDBe Search • Name Search • Fragment Search • Structure Search

  11. Name Search

  12. Name Search

  13. RCSB vs PDBe • There are some differences between PDBe and RCSB PDB. • For example: • Ribose-PDBe-31 RCSB-27 • Ribitol – PDBe-45 RCSB-44 • Neuraminic Acid- PDBe-15 RCSB-14 • Updated to PDBe-16 RCSB-15 as of 6/29

  14. Fragment Search

  15. Search Results

  16. Structure Search (SMILE)

  17. Search Results

  18. Remaining Questions • Are we including any form of straight chain carbohydrates in the searches? • “itol” sugar alcohols • Acids • Less than C5

  19. Oxygen involved in linkage SMD OBN

  20. Double-bonded O LGC AFN

  21. Missing hydroxyl RF5 GC1

  22. Hydroxyl substitution 20X TIA

  23. Multiple rings LKC AB0

  24. Thio and azasugars L37 SSD MA1

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