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Loganic Acid

PubChem CID
89640
Structure
Loganic Acid_small.png
Loganic Acid_3D_Structure.png
Molecular Formula
Synonyms
  • Loganic acid
  • 22255-40-9
  • Loganin acid
  • (1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid
  • CHEBI:30632
Molecular Weight
376.36 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-11
Description
Loganic acid is a cyclopentapyran that is 1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid substituted at positions 1, 6 and 7 by beta-D-glucosyloxy, hydroxy and methyl groups respectively It has a role as a plant metabolite. It is a cyclopentapyran, an alpha,beta-unsaturated monocarboxylic acid and a glucoside. It is a conjugate acid of a loganate.
Loganic acid has been reported in Gentiana macrophylla, Gentiana thunbergii, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Loganic Acid.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

(1S,4aS,6S,7R,7aS)-6-hydroxy-7-methyl-1-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-4-carboxylic acid
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C16H24O10/c1-5-8(18)2-6-7(14(22)23)4-24-15(10(5)6)26-16-13(21)12(20)11(19)9(3-17)25-16/h4-6,8-13,15-21H,2-3H2,1H3,(H,22,23)/t5-,6+,8-,9+,10+,11+,12-,13+,15-,16-/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

JNNGEAWILNVFFD-CDJYTOATSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

C[C@H]1[C@H](C[C@H]2[C@@H]1[C@@H](OC=C2C(=O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C16H24O10
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

2.3.2 European Community (EC) Number

2.3.3 UNII

2.3.4 ChEBI ID

2.3.5 ChEMBL ID

2.3.6 DSSTox Substance ID

2.3.7 KEGG ID

2.3.8 Lipid Maps ID (LM_ID)

2.3.9 Metabolomics Workbench ID

2.3.10 Nikkaji Number

2.3.11 Wikidata

2.3.12 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • 8-epiloganic acid
  • loganic acid

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
376.36 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-1.7
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
10
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
376.13694696 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
376.13694696 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
166 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
26
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
565
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
10
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

3.2 Chemical Classes

3.2.1 Lipids

Lipids -> Prenol Lipids [PR] -> Isoprenoids [PR01] -> C10 isoprenoids (monoterpenes) [PR0102]

4 Spectral Information

4.1 1D NMR Spectra

4.1.1 13C NMR Spectra

Copyright
Copyright © 1980, 1981-2024 John Wiley & Sons, Inc. All Rights Reserved.
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4.2 Mass Spectrometry

4.2.1 LC-MS

1 of 3
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MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
377.1442
Instrument
Agilent 6530 Q-TOF
Instrument Type
LC-ESI-QTOF
Ionization Mode
positive
Collision Energy
40 V
Retention Time
0.486
Top 5 Peaks

84.9595 100

162.9683 14.17

84.9669 13.24

162.9786 13.03

61.0106 12.12

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2 of 3
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MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
377.1442
Instrument
Agilent 6530 Q-TOF
Instrument Type
LC-ESI-QTOF
Ionization Mode
positive
Collision Energy
20 V
Retention Time
0.486
Top 5 Peaks

162.9698 100

162.9762 72.88

377.1403 45.30

197.0788 43.23

84.9572 24.43

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4.2.2 Other MS

1 of 3
View All
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
375.1296705
Ionization Mode
negative
Retention Time
1.691176308
Top 5 Peaks

179.03357 0.29

201.015541 0.18

161.023022 0.08

135.04398 0.06

213.075282 0.06

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2 of 3
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MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M+Na]+
Precursor m/z
399.126165
Ionization Mode
positive
Retention Time
1.689039225
Top 5 Peaks

237.03704 0.36

219.024381 0.34

225.013784 0.22

185.020998 0.02

201.014561 0.02

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6 Chemical Vendors

7 Literature

7.1 Consolidated References

7.2 NLM Curated PubMed Citations

7.3 Springer Nature References

7.4 Chemical Co-Occurrences in Literature

7.5 Chemical-Gene Co-Occurrences in Literature

7.6 Chemical-Disease Co-Occurrences in Literature

8 Patents

8.1 Depositor-Supplied Patent Identifiers

9 Interactions and Pathways

9.1 Protein Bound 3D Structures

9.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

10 Biological Test Results

10.1 BioAssay Results

11 Taxonomy

The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

12 Classification

12.1 MeSH Tree

12.2 ChEBI Ontology

12.3 LIPID MAPS Classification

12.4 KEGG: Lipid

12.5 KEGG: Phytochemical Compounds

12.6 KEGG : Glycosides

12.7 ChemIDplus

12.8 ChEMBL Target Tree

12.9 EPA DSSTox Classification

12.10 LOTUS Tree

12.11 MolGenie Organic Chemistry Ontology

13 Information Sources

  1. CAS Common Chemistry
    LICENSE
    The data from CAS Common Chemistry is provided under a CC-BY-NC 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc/4.0/
  2. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  4. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
    [1S-(1α,4aα,6α,7α,7aα)]-1-(β-D-glucopyranosyloxy)-1,4a,5,6,7,7a-hexahydro-6-hydroxy-7-methylcyclopenta[c]pyran-4-carboxylic acid
    https://echa.europa.eu/substance-information/-/substanceinfo/100.040.781
  5. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  6. ChEBI
  7. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  8. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  9. Japan Chemical Substance Dictionary (Nikkaji)
  10. KEGG
    LICENSE
    Academic users may freely use the KEGG website. Non-academic use of KEGG generally requires a commercial license
    https://www.kegg.jp/kegg/legal.html
  11. LIPID MAPS
    Lipid Classification
    https://www.lipidmaps.org/
  12. Natural Product Activity and Species Source (NPASS)
  13. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  14. Metabolomics Workbench
  15. Protein Data Bank in Europe (PDBe)
  16. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  17. SpectraBase
  18. Springer Nature
  19. Wikidata
  20. Wikipedia
  21. PubChem
  22. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
  23. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  24. NCBI
CONTENTS