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Rubiadin

PubChem CID
124062
Structure
Rubiadin_small.png
Rubiadin_3D_Structure.png
Rubiadin__Crystal_Structure.png
Molecular Formula
Synonyms
  • Rubiadin
  • 117-02-2
  • 1,3-dihydroxy-2-methylanthracene-9,10-dione
  • 9,10-Anthracenedione, 1,3-dihydroxy-2-methyl-
  • Rubiadine
Molecular Weight
254.24 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-06-24
  • Modify:
    2025-01-11
Description
Rubiadin is a dihydroxyanthraquinone that is anthracene-9,10-dione substituted by hydroxy groups at positions 1 and 3 and a methyl group at position 2. It has been isolated from Rubia yunnanensis. It has a role as an antibacterial agent, an antioxidant, a hepatoprotective agent and a plant metabolite.
Rubiadin has been reported in Rubia lanceolata, Rubia wallichiana, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Rubiadin.png

1.2 3D Conformer

1.3 Crystal Structures

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CCDC Number
Crystal Structure Data
Crystal Structure Depiction
Crystal Structure Depiction

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

1,3-dihydroxy-2-methylanthracene-9,10-dione
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C15H10O4/c1-7-11(16)6-10-12(13(7)17)15(19)9-5-3-2-4-8(9)14(10)18/h2-6,16-17H,1H3
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

IRZTUXPRIUZXMP-UHFFFAOYSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

CC1=C(C=C2C(=C1O)C(=O)C3=CC=CC=C3C2=O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C15H10O4
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 HMDB ID

2.3.8 KEGG ID

2.3.9 Lipid Maps ID (LM_ID)

2.3.10 Metabolomics Workbench ID

2.3.11 Nikkaji Number

2.3.12 Wikidata

2.3.13 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • 1,3-dihydroxy-2-methyl-9,10-anthracenedione
  • rubiadin

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
254.24 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
3.1
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
2
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
4
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
0
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
254.05790880 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
254.05790880 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
74.6 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
19
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
405
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
0
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 SpringerMaterials Properties

3.3 Chemical Classes

3.3.1 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

3.3.2 Lipids

Polyketides [PK] -> Aromatic polyketides [PK13] -> Anthracenes and phenanthrenes [PK1304]

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
E1-40-1505-13
Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
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4.2.2 MS-MS

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Spectra ID
Ionization Mode
Negative
Top 5 Peaks

224.0475 100

225.0551 80.36

223.0395 53.91

210.0319 34.74

195.0446 20.38

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Spectra ID
Ionization Mode
Negative
Top 5 Peaks

253.0502 100

225.0553 33.94

209.0603 11.16

224.0466 3.38

208.0527 2.69

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4.2.3 LC-MS

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MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
255.0652
Instrument
Agilent 6530 Q-TOF
Instrument Type
LC-ESI-QTOF
Ionization Mode
positive
Collision Energy
40 V
Retention Time
5.7075
Top 5 Peaks

115.0543 100

152.062 83.53

143.0494 60.12

105.0338 55.20

83.0135 34.78

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MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
255.0652
Instrument
Agilent 6530 Q-TOF
Instrument Type
LC-ESI-QTOF
Ionization Mode
positive
Collision Energy
20 V
Retention Time
5.7075
Top 5 Peaks

255.0652 100

199.0392 45.55

171.0446 11.47

143.0491 3.44

83.013 3.40

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4.2.4 Other MS

MS Category
Experimental
MS Type
Other
Precursor Type
[M-H]-
Top 5 Peaks

253.05047607421875 6944104

225.05535888671875 1900376.50

224.04751586914062 558720.06

209.0605010986328 525980.62

208.0529022216797 288319.09

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6 Chemical Vendors

7 Safety and Hazards

7.1 Hazards Identification

7.1.1 GHS Classification

Pictogram(s)
Irritant
Signal
Warning
GHS Hazard Statements
H302 (100%): Harmful if swallowed [Warning Acute toxicity, oral]
Precautionary Statement Codes

P264, P270, P301+P317, P330, and P501

(The corresponding statement to each P-code can be found at the GHS Classification page.)

ECHA C&L Notifications Summary

Aggregated GHS information provided per 39 reports by companies from 2 notifications to the ECHA C&L Inventory.

Information may vary between notifications depending on impurities, additives, and other factors. The percentage value in parenthesis indicates the notified classification ratio from companies that provide hazard codes. Only hazard codes with percentage values above 10% are shown.

7.1.2 Hazard Classes and Categories

Acute Tox. 4 (100%)

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
S29 | PHYTOTOXINS | Toxic Plant Phytotoxin (TPPT) Database | DOI:10.5281/zenodo.2652993

13 Classification

13.1 MeSH Tree

13.2 ChEBI Ontology

13.3 LIPID MAPS Classification

13.4 KEGG: Lipid

13.5 KEGG: Phytochemical Compounds

13.6 ChemIDplus

13.7 UN GHS Classification

13.8 NORMAN Suspect List Exchange Classification

13.9 EPA DSSTox Classification

13.10 LOTUS Tree

13.11 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/
  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. Crystallography Open Database (COD)
    LICENSE
    All data in the COD and the database itself are dedicated to the public domain and licensed under the CC0 License. Users of the data should acknowledge the original authors of the structural data.
    https://creativecommons.org/publicdomain/zero/1.0/
  11. The Cambridge Structural Database
  12. 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
  13. Japan Chemical Substance Dictionary (Nikkaji)
  14. 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
  15. KNApSAcK Species-Metabolite Database
  16. Natural Product Activity and Species Source (NPASS)
  17. 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/
    Rubiadin
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  18. LIPID MAPS
    Lipid Classification
    https://www.lipidmaps.org/
  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. SpectraBase
  22. Springer Nature
  23. SpringerMaterials
  24. Wikidata
  25. Wikipedia
  26. PubChem
  27. 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
  28. GHS Classification (UNECE)
  29. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  30. PATENTSCOPE (WIPO)
CONTENTS