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Sugar Searching Methods

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

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Sugar Searching Methods

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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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