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Cubebin

PubChem CID
117443
Structure
Cubebin_small.png
Cubebin_3D_Structure.png
Molecular Formula
Synonyms
  • Cubebin
  • (-)-Cubebin
  • 18423-69-3
  • beta-cubebin
  • .beta.-Cubebin
Molecular Weight
356.4 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-06-24
  • Modify:
    2025-01-11
Description
(-)-cubebin is a lignan that consists of tetrahydrofuran-2-ol substituted by two 1,3-benzodioxol-5-ylmethyl groups at positions 3 and 4 respectively (the 2S,3R,4R stereoisomer). It is isolated from the leaves of Piper nigrum and exhibits analgesic, anti-inflammatory, antimicrobial and trypanocidal activities. It has a role as an antimicrobial agent, a trypanocidal drug, an anti-inflammatory agent, an analgesic, a histamine antagonist and a plant metabolite. It is a lignan, a member of benzodioxoles, a secondary alcohol, a cyclic acetal and a lactol.
Cubebin has been reported in Aristolochia triangularis, Aristolochia galeata, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Cubebin.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

(2S,3R,4R)-3,4-bis(1,3-benzodioxol-5-ylmethyl)oxolan-2-ol
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C20H20O6/c21-20-15(6-13-2-4-17-19(8-13)26-11-24-17)14(9-22-20)5-12-1-3-16-18(7-12)25-10-23-16/h1-4,7-8,14-15,20-21H,5-6,9-11H2/t14-,15+,20-/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

DIYWRNLYKJKHAM-MDOVXXIYSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

C1[C@@H]([C@H]([C@H](O1)O)CC2=CC3=C(C=C2)OCO3)CC4=CC5=C(C=C4)OCO5
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C20H20O6
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 Metabolomics Workbench ID

2.3.9 Nikkaji Number

2.3.10 Wikidata

2.4 Synonyms

2.4.1 MeSH Entry Terms

cubebin

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
356.4 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
3.4
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
1
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
6
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
356.12598835 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
356.12598835 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
66.4 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
487
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
3
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)

4 Spectral Information

4.1 1D NMR Spectra

4.1.1 13C NMR Spectra

1 of 2
Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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2 of 2
Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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4.2 Mass Spectrometry

4.2.1 GC-MS

Source of Spectrum
RCM-22-2663-Cubebin
Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
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6 Chemical Vendors

7 Associated Disorders and Diseases

8 Literature

8.1 Consolidated References

8.2 NLM Curated PubMed Citations

8.3 Springer Nature References

8.4 Chemical Co-Occurrences in Literature

8.5 Chemical-Gene Co-Occurrences in Literature

8.6 Chemical-Disease Co-Occurrences in Literature

9 Patents

9.1 Depositor-Supplied Patent Identifiers

9.2 WIPO PATENTSCOPE

9.3 Chemical Co-Occurrences in Patents

9.4 Chemical-Disease Co-Occurrences in Patents

9.5 Chemical-Gene Co-Occurrences in Patents

10 Interactions and Pathways

10.1 Chemical-Target Interactions

11 Biological Test Results

11.1 BioAssay Results

12 Taxonomy

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

13 Classification

13.1 MeSH Tree

13.2 ChEBI Ontology

13.3 ChemIDplus

13.4 ChEMBL Target Tree

13.5 EPA DSSTox Classification

13.6 LOTUS Tree

13.7 MolGenie Organic Chemistry Ontology

14 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/
    (2S,3R,4R)-3,4-Bis(1,3-benzodioxol-5-ylmethyl)tetrahydro-2-furanol
    https://commonchemistry.cas.org/detail?cas_rn=18423-69-3
  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
  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. Comparative Toxicogenomics Database (CTD)
    LICENSE
    It is to be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of NC State University.
    http://ctdbase.org/about/legal.jsp
  10. Japan Chemical Substance Dictionary (Nikkaji)
  11. 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
  12. Natural Product Activity and Species Source (NPASS)
  13. Metabolomics Workbench
  14. SpectraBase
    (8-R,8'-R,9-S)-9-HYDROXY-3,4,3',4'-DIMETHYLENEDIOXY-8.8',9.O.9'-LIGNAN-DELTA:1,3,5,1',3',5'
    https://spectrabase.com/spectrum/AlaJmQLB4Im
  15. Springer Nature
  16. Therapeutic Target Database (TTD)
  17. Wikidata
  18. PubChem
  19. 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
  20. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  21. PATENTSCOPE (WIPO)
CONTENTS