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Secoisolariciresinol

PubChem CID
65373
Structure
Secoisolariciresinol_small.png
Secoisolariciresinol_3D_Structure.png
Secoisolariciresinol__Crystal_Structure.png
Molecular Formula
Synonyms
  • Secoisolariciresinol
  • 29388-59-8
  • (-)-Secoisolariciresinol
  • (2R,3R)-2,3-bis[(4-hydroxy-3-methoxyphenyl)methyl]butane-1,4-diol
  • 1,4-Butanediol, 2,3-bis[(4-hydroxy-3-methoxyphenyl)methyl]-, (2R,3R)-
Molecular Weight
362.4 g/mol
Computed by PubChem 2.2 (PubChem release 2024.11.20)
Dates
  • Create:
    2005-08-01
  • Modify:
    2025-01-18
Description
(-)-secoisolariciresinol is an enantiomer of secoisolariciresinol having (-)-(2R,3R)-configuration. It has a role as an antidepressant, a plant metabolite and a phytoestrogen. It is an enantiomer of a (+)-secoisolariciresinol.
Secoisolariciresinol has been used in trials studying the prevention of Breast Cancer.
Secoisolariciresinol has been reported in Camellia sinensis, Raphanus sativus var. sativus, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Secoisolariciresinol.png

1.2 3D Conformer

1.3 Crystal Structures

CCDC Number
Crystal Structure Data
Crystal Structure Depiction
Crystal Structure Depiction

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

(2R,3R)-2,3-bis[(4-hydroxy-3-methoxyphenyl)methyl]butane-1,4-diol
Computed by Lexichem TK 2.7.0 (PubChem release 2024.11.20)

2.1.2 InChI

InChI=1S/C20H26O6/c1-25-19-9-13(3-5-17(19)23)7-15(11-21)16(12-22)8-14-4-6-18(24)20(10-14)26-2/h3-6,9-10,15-16,21-24H,7-8,11-12H2,1-2H3/t15-,16-/m0/s1
Computed by InChI 1.07.0 (PubChem release 2024.11.20)

2.1.3 InChIKey

PUETUDUXMCLALY-HOTGVXAUSA-N
Computed by InChI 1.07.0 (PubChem release 2024.11.20)

2.1.4 SMILES

COC1=C(C=CC(=C1)C[C@@H](CO)[C@@H](CC2=CC(=C(C=C2)O)OC)CO)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C20H26O6
Computed by PubChem 2.2 (PubChem release 2024.11.20)

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 DrugBank ID

2.3.7 DSSTox Substance ID

2.3.8 HMDB ID

2.3.9 KEGG ID

2.3.10 Metabolomics Workbench ID

2.3.11 NCI Thesaurus Code

2.3.12 Nikkaji Number

2.3.13 Wikidata

2.3.14 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • 2,3-bis((4-hydroxy-3-methoxyphenyl)methyl)-1,4-butanediol
  • knotolan
  • secoisolariciresinol
  • secoisolariciresinol, (R*,S*)-isomer

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
362.4 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2024.11.20)
Property Name
XLogP3-AA
Property Value
2.5
Reference
Computed by XLogP3 3.0 (PubChem release 2024.11.20)
Property Name
Hydrogen Bond Donor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2024.11.20)
Property Name
Hydrogen Bond Acceptor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2024.11.20)
Property Name
Rotatable Bond Count
Property Value
9
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2024.11.20)
Property Name
Exact Mass
Property Value
362.17293854 Da
Reference
Computed by PubChem 2.2 (PubChem release 2024.11.20)
Property Name
Monoisotopic Mass
Property Value
362.17293854 Da
Reference
Computed by PubChem 2.2 (PubChem release 2024.11.20)
Property Name
Topological Polar Surface Area
Property Value
99.4 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2024.11.20)
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
356
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2024.11.20)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
2
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 Drugs

Pharmaceuticals -> Listed in ZINC15
S55 | ZINC15PHARMA | Pharmaceuticals from ZINC15 | DOI:10.5281/zenodo.3247749

3.2.2 Endocrine Disruptors

Potential endocrine disrupting compound
S109 | PARCEDC | List of 7074 potential endocrine disrupting compounds (EDCs) by PARC T4.2 | DOI:10.5281/zenodo.10944198

4 Spectral Information

4.1 Mass Spectrometry

4.1.1 GC-MS

1 of 2
Source of Spectrum
E1-39-92-11
Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
Thumbnail
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2 of 2
Source of Spectrum
D1-2006-1782-2
Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
Thumbnail
Thumbnail

4.1.2 MS-MS

1 of 6
View All
Spectra ID
Ionization Mode
Positive
Top 5 Peaks

122.03574 100

137.05365 96.20

138.07034 50.60

131.04947 46.80

116.06033 34.20

Thumbnail
Thumbnail
2 of 6
View All
Spectra ID
Ionization Mode
Positive
Top 5 Peaks

137.06427 100

131.0546 35.20

124.04817 28.60

236.12799 28.60

133.06233 26.40

Thumbnail
Thumbnail

4.1.3 LC-MS

1 of 17
View All
Authors
Tetsuya Mori, Center for Sustainable Resource Science, RIKEN
Instrument
LC, Waters Acquity UPLC System; MS, Waters Xevo G2 Q-Tof
Instrument Type
LC-ESI-QTOF
MS Level
MS2
Ionization Mode
POSITIVE
Ionization
ESI
Collision Energy
6V
Column Name
Acquity bridged ethyl hybrid C18 (1.7 um, 2.1 mm * 100 mm, Waters)
Retention Time
4.76425
Precursor m/z
363.180215
Precursor Adduct
[M+H]+
Top 5 Peaks

137.05693 999

327.16397 640

163.07758 349

133.06633 302

138.0636 255

Thumbnail
Thumbnail
License
CC BY-NC-SA
Reference
Tsugawa H., Nakabayashi R., Mori T., Yamada Y., Takahashi M., Rai A., Sugiyama R., Yamamoto H., Nakaya T., Yamazaki M., Kooke R., Bac-Molenaar JA., Oztolan-Erol N., Keurentjes JJB., Arita M., Saito K. (2019) "A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms" Nature Methods 16(4):295-298. [doi:10.1038/s41592-019-0358-2]
2 of 17
View All
Authors
Tetsuya Mori, Center for Sustainable Resource Science, RIKEN
Instrument
LC, Waters Acquity UPLC System; MS, Waters Xevo G2 Q-Tof
Instrument Type
LC-ESI-QTOF
MS Level
MS2
Ionization Mode
POSITIVE
Ionization
ESI
Collision Energy
6V
Column Name
Acquity bridged ethyl hybrid C18 (1.7 um, 2.1 mm * 100 mm, Waters)
Retention Time
4.76425
Precursor m/z
363.180215
Precursor Adduct
[M+H]+
Top 5 Peaks

137.05914 999

163.07651 200

133.06491 170

131.05063 162

122.03461 111

Thumbnail
Thumbnail
License
CC BY-NC-SA
Reference
Tsugawa H., Nakabayashi R., Mori T., Yamada Y., Takahashi M., Rai A., Sugiyama R., Yamamoto H., Nakaya T., Yamazaki M., Kooke R., Bac-Molenaar JA., Oztolan-Erol N., Keurentjes JJB., Arita M., Saito K. (2019) "A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms" Nature Methods 16(4):295-298. [doi:10.1038/s41592-019-0358-2]

6 Chemical Vendors

7 Drug and Medication Information

7.1 Drug Indication

7.2 Clinical Trials

7.2.1 ClinicalTrials.gov

8 Food Additives and Ingredients

8.1 Associated Foods

9 Pharmacology and Biochemistry

9.1 MeSH Pharmacological Classification

Phytoestrogens
Compounds derived from plants, primarily ISOFLAVONES that mimic or modulate endogenous estrogens, usually by binding to ESTROGEN RECEPTORS. (See all compounds classified as Phytoestrogens.)

9.2 Human Metabolite Information

9.2.1 Cellular Locations

Membrane

9.3 Biochemical Reactions

10 Associated Disorders and Diseases

11 Literature

11.1 Consolidated References

11.2 NLM Curated PubMed Citations

11.3 Springer Nature References

11.4 Thieme References

11.5 Chemical Co-Occurrences in Literature

11.6 Chemical-Gene Co-Occurrences in Literature

11.7 Chemical-Disease Co-Occurrences in Literature

12 Patents

12.1 Depositor-Supplied Patent Identifiers

12.2 WIPO PATENTSCOPE

12.3 Chemical Co-Occurrences in Patents

12.4 Chemical-Disease Co-Occurrences in Patents

12.5 Chemical-Gene Co-Occurrences in Patents

13 Interactions and Pathways

13.1 Protein Bound 3D Structures

13.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

13.2 Chemical-Target Interactions

13.3 Pathways

14 Biological Test Results

14.1 BioAssay Results

15 Taxonomy

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

16 Classification

16.1 MeSH Tree

16.2 NCI Thesaurus Tree

16.3 ChEBI Ontology

16.4 KEGG: Phytochemical Compounds

16.5 ChemIDplus

16.6 ChEMBL Target Tree

16.7 NORMAN Suspect List Exchange Classification

16.8 EPA DSSTox Classification

16.9 LOTUS Tree

16.10 MolGenie Organic Chemistry Ontology

17 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. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
  4. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. 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
    [R-(R*,R*)]-2,3-bis[(4-hydroxy-3-methoxyphenyl)methyl]butane-1,4-diol
    https://echa.europa.eu/substance-information/-/substanceinfo/100.045.076
  6. 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
  7. Human Metabolome Database (HMDB)
    LICENSE
    HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
    http://www.hmdb.ca/citing
  8. ChEBI
  9. 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/
  10. Open Targets
    LICENSE
    Datasets generated by the Open Targets Platform are freely available for download.
    https://platform-docs.opentargets.org/licence
  11. 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
  12. ClinicalTrials.gov
    LICENSE
    The ClinicalTrials.gov data carry an international copyright outside the United States and its Territories or Possessions. Some ClinicalTrials.gov data may be subject to the copyright of third parties; you should consult these entities for any additional terms of use.
    https://clinicaltrials.gov/ct2/about-site/terms-conditions#Use
  13. 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
  14. FooDB
    LICENSE
    FooDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (FooDB) and the original publication.
    https://foodb.ca/about
    (+)-Secoisolariciresinol
    https://foodb.ca/compounds/FDB001441
    (8R,8'R)-Secoisolariciresinol
    https://foodb.ca/compounds/FDB021314
  15. Japan Chemical Substance Dictionary (Nikkaji)
  16. 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
  17. Natural Product Activity and Species Source (NPASS)
  18. MassBank Europe
  19. 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
  20. Metabolomics Workbench
  21. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  22. NORMAN Suspect List Exchange
    LICENSE
    Data: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    Secoisolariciresinol
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  23. Protein Data Bank in Europe (PDBe)
  24. 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
  25. Rhea - Annotated Reactions Database
    LICENSE
    Rhea has chosen to apply the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/). This means that you are free to copy, distribute, display and make commercial use of the database in all legislations, provided you credit (cite) Rhea.
    https://www.rhea-db.org/help/license-disclaimer
  26. SpectraBase
    (2R,3R)-2,3-bis[(3-methoxy-4-oxidanyl-phenyl)methyl]butane-1,4-diol
    https://spectrabase.com/spectrum/FWaTAHJ4U9t
    (2R,3R)-2,3-bis[(3-methoxy-4-oxidanyl-phenyl)methyl]butane-1,4-diol
    https://spectrabase.com/spectrum/L3USPxQAPun
  27. Springer Nature
  28. The Cambridge Structural Database
  29. Thieme Chemistry
    LICENSE
    The Thieme Chemistry contribution within PubChem is provided under a CC-BY-NC-ND 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc-nd/4.0/
  30. Wikidata
  31. Wikipedia
  32. PubChem
  33. 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
  34. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  35. PATENTSCOPE (WIPO)
  36. NCBI
CONTENTS