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PubChem

(+)-Genipin

PubChem CID
442424
Structure
(+)-Genipin_small.png
(+)-Genipin_3D_Structure.png
Molecular Formula
Synonyms
  • Genipin
  • 6902-77-8
  • (+)-Genipin
  • methyl (1R,4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-1,4a,5,7a-tetrahydrocyclopenta[c]pyran-4-carboxylate
  • A3V2NE52YG
Molecular Weight
226.23 g/mol
Computed by PubChem 2.2 (PubChem release 2025.04.14)
Dates
  • Create:
    2005-06-24
  • Modify:
    2026-05-17
Description
Genipin is an iridoid monoterpenoid. It has a role as an uncoupling protein inhibitor, an antioxidant, a cross-linking reagent, a hepatotoxic agent, an anti-inflammatory agent and an apoptosis inhibitor.
Genipin is under investigation in clinical trial NCT05755750 (Intratendinous Genipin Injection in Horses With Tendon Injuries).
Genipin has been reported in Gardenia jasminoides, Eucommia ulmoides, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
(+)-Genipin.png

1.2 3D Conformer

Interactive Chemical Structure Model
Conformer of 10

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

methyl (1R,4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-1,4a,5,7a-tetrahydrocyclopenta[c]pyran-4-carboxylate
Computed by Lexichem TK 2.7.0 (PubChem release 2025.04.14)

2.1.2 InChI

InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3/t7-,9-,11-/m1/s1
Computed by InChI 1.07.2 (PubChem release 2025.04.14)

2.1.3 InChIKey

AZKVWQKMDGGDSV-BCMRRPTOSA-N
Computed by InChI 1.07.2 (PubChem release 2025.04.14)

2.1.4 SMILES

COC(=O)C1=CO[C@H]([C@H]2[C@@H]1CC=C2CO)O
Computed by OEChem 2.3.0 (PubChem release 2025.04.14)

2.2 Molecular Formula

C11H14O5
Computed by PubChem 2.2 (PubChem release 2025.04.14)

2.3 Other Identifiers

2.3.1 CAS

2.3.2 Deprecated CAS

1202641-87-9

2.3.3 European Community (EC) Number

2.3.4 UNII

2.3.5 AIDS Number

2.3.6 ChEBI ID

2.3.7 ChEMBL ID

2.3.8 DrugBank ID

2.3.9 DSSTox Substance ID

2.3.10 KEGG ID

2.3.11 Lipid Maps ID (LM_ID)

2.3.12 Metabolomics Workbench ID

2.3.13 Nikkaji Number

2.3.14 Wikidata

2.3.15 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

genipin

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
226.23 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2025.04.14)
Property Name
XLogP3-AA
Property Value
-0.7
Reference
Computed by XLogP3 3.0 (PubChem release 2025.04.14)
Property Name
Hydrogen Bond Donor Count
Property Value
2
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2025.04.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
5
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2025.04.14)
Property Name
Rotatable Bond Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2025.04.14)
Property Name
Exact Mass
Property Value
226.08412354 Da
Reference
Computed by PubChem 2.2 (PubChem release 2025.04.14)
Property Name
Monoisotopic Mass
Property Value
226.08412354 Da
Reference
Computed by PubChem 2.2 (PubChem release 2025.04.14)
Property Name
Topological Polar Surface Area
Property Value
76 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2025.04.14)
Property Name
Heavy Atom Count
Property Value
16
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
357
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2025.04.14)
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 2025.04.14)

3.2 Chemical Classes

3.2.1 Lipids

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

4 Spectral Information

4.1 Mass Spectrometry

4.1.1 GC-MS

1 of 2 items
MoNA ID
MS Category
Experimental
MS Type
GC-MS
MS Level
MS1
Instrument
HITACHI M-80
Instrument Type
EI-B
Ionization Mode
positive
Top 5 Peaks

91 99.99

148 79.82

78 77.66

120 63.24

39 61.36

Thumbnail
Thumbnail
License
CC BY-NC-SA
2 of 2 items
Source of Spectrum
G4-59-1170-1
Copyright
Copyright © 2020-2025 John Wiley & Sons, Inc. All Rights Reserved.
Thumbnail
Thumbnail

4.1.2 LC-MS

1 of 3 items
View All
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
225.076843261719
Instrument
Agilent 6550 iFunnel
Instrument Type
LC-ESI-QTOF
Ionization
ESI
Ionization Mode
negative
Collision Energy
20
Retention Time
1.09
Top 5 Peaks

68.99848 100

101.0258 69.73

147.0501 31.58

105.0368 14.76

123.0493 12.52

Thumbnail
Thumbnail
License
CC-BY
2 of 3 items
View All
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
225.076843261719
Instrument
Agilent 6550 iFunnel
Instrument Type
LC-ESI-QTOF
Ionization
ESI
Ionization Mode
negative
Collision Energy
30
Retention Time
1.1
Top 5 Peaks

68.99848 100

101.0258 13.70

147.0459 9.58

41.00467 8.19

105.0368 5.07

Thumbnail
Thumbnail
License
CC-BY

4.1.3 Other MS

Authors
NARA WOMEN'S UNIVERSITY
Instrument
HITACHI M-80
Instrument Type
EI-B
MS Level
MS
Ionization Mode
POSITIVE
Ionization
ENERGY 70 eV
Top 5 Peaks

91 999

148 798

78 777

120 632

39 614

Thumbnail
Thumbnail
License
CC BY-NC-SA

6 Chemical Vendors

66 vendors
PubChem SID: 442118678
Purchasable Chemical: AS144249
PubChem SID: 492840696
Purchasable Chemical: MCULE-2950840149
PubChem SID: 252952400
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PubChem SID: 434337804
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PubChem SID: 387060811
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PubChem SID: 354271670
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PubChem SID: 521605238
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PubChem SID: 473805142
Purchasable Chemical: EN300-7409283
PubChem SID: 475521300
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PubChem SID: 252160151
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PubChem SID: 251917145
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PubChem SID: 251915797
Purchasable Chemical: 6902-77-8
PubChem SID: 527690726
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PubChem SID: 527705451
Purchasable Chemical: ACM6902778-3
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PubChem SID: 497159031
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PubChem SID: 377510378
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PubChem SID: 470691697
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PubChem SID: 123847688
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PubChem SID: 523957384
Purchasable Chemical: 6902-77-8
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PubChem SID: 347913420
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PubChem SID: 254761659
Purchasable Chemical: 6902-77-8
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Purchasable Chemical: NP3880
CATO Research Chemicals Inc. (Chemical Vendors, Research and Development)
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PubChem SID: 506202486
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PubChem SID: 517817410
Purchasable Chemical: ACIDLC759
PubChem SID: 445658956
Purchasable Chemical: 40457

7 Drug and Medication Information

7.1 Drug Indication

1 item
MeSH Heading
EFO Term
Max Phase
Phase 3

7.2 Clinical Trials

7.2.1 ClinicalTrials.gov

1 item
  • Intratendinous Genipin Injection in Horses With Tendon Injuries
    Phase: Phase 3
    Status: Completed
    Date: 2023-03-06

7.3 Drug Development Summary

Max Phase
Phase 3

8 Pharmacology and Biochemistry

8.1 MeSH Pharmacological Classification

Cholagogues and Choleretics
Gastrointestinal agents that stimulate the flow of bile into the duodenum (cholagogues) or stimulate the production of bile by the liver (choleretic).

9 Safety and Hazards

9.1 Hazards Identification

9.1.1 GHS Classification

Pictogram(s)
Acute Toxic
Signal
Danger
GHS Hazard Statements
H301 (100%): Toxic if swallowed [Danger Acute toxicity, oral]
Precautionary Statement Codes
ECHA C&L Notifications Summary

Aggregated GHS information provided per 52 reports by companies from 7 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. For more detailed information, please visit ECHA C&L website.

9.1.2 Hazard Classes and Categories

Acute Tox. 3 (100%)

9.2 Regulatory Information

REACH Registered Substance

10 Toxicity

10.1 Toxicological Information

10.1.1 Acute Effects

4 items
Compound CID
Organism
mouse
Test Type
LD50
Route
oral
Dose
237 mg/kg
Reference
Yakugaku Zasshi. Journal of Pharmacy., 94(157), 1974 [PMID:4859051]
Compound CID
Organism
mouse
Test Type
LD50
Route
intravenous
Dose
153 mg/kg
Reference
Yakugaku Zasshi. Journal of Pharmacy., 94(157), 1974 [PMID:4859051]
Compound CID
Organism
rat
Test Type
LD
Route
oral
Dose
>50 mg/kg
Reference
Oyo Yakuri. Pharmacometrics., 19(259), 1980
Compound CID
Organism
mouse
Test Type
LD50
Route
intraperitoneal
Dose
190 mg/kg
Reference
Yakugaku Zasshi. Journal of Pharmacy., 94(157), 1974 [PMID:4859051]

11 Associated Disorders and Diseases

6 items
Page of 2

12 Literature

12.1 Consolidated References

2,535 items
Page of 507

12.2 NLM Curated PubMed Citations

12.3 Springer Nature References

1,525 items
Page of 305

12.4 Chemical Co-Occurrences in Literature

Chemical
Selected evidence
391 articles
View All
Chemical
Selected evidence
632 articles
View All
Chemical
Selected evidence
322 articles
View All

12.5 Chemical-Gene Co-Occurrences in Literature

Gene/Protein/Enzyme
Selected evidence
134 articles
View All
Gene/Protein/Enzyme
Selected evidence
32 articles
View All
Gene/Protein/Enzyme
Selected evidence
60 articles
View All

12.6 Chemical-Disease Co-Occurrences in Literature

Disease
Selected evidence
284 articles
View All
Disease
Selected evidence
342 articles
View All
Disease
Selected evidence
211 articles
View All

12.7 Chemical-Organism Co-Occurrences in Literature

Organism
Selected evidence
124 articles
View All
Organism
Selected evidence
101 articles
View All
Organism
Selected evidence
316 articles
View All

13 Patents

13.1 Depositor-Supplied Patent Identifiers

12,629 items
Page of 2,526

13.2 WIPO PATENTSCOPE

13.3 Chemical Co-Occurrences in Patents

13.4 Chemical-Disease Co-Occurrences in Patents

Disease
Selected evidence
270 patents from 185 patent families
View All
Disease
Selected evidence
292 patents from 182 patent families
View All
Disease
Selected evidence
60 patents from 43 patent families
View All

13.5 Chemical-Gene Co-Occurrences in Patents

Gene
Selected evidence
316 patents from 194 patent families
View All
Gene
Selected evidence
125 patents from 80 patent families
View All

13.6 Chemical-Organism Co-Occurrences in Patents

Organism
Selected evidence
101 patents from 67 patent families
View All
Organism
Selected evidence
31 patents from 14 patent families
View All
Organism
Selected evidence
504 patents from 326 patent families
View All

14 Interactions and Pathways

14.1 Chemical-Target Interactions

94 items
Gene
Taxonomy
Action
Genipin results in increased secretion of TNF protein
Evidence
Data Source
Gene
Taxonomy
Action
Genipin inhibits the reaction [lipopolysaccharides results in increased expression of CD14 mrna]
Evidence
Data Source
Gene
Taxonomy
Action
Genipin inhibits the reaction [lipopolysaccharides results in increased expression of CXCL5 mrna]
Evidence
Data Source
Gene
Taxonomy
Action
Genipin inhibits the reaction [lipopolysaccharides results in increased expression of GBP7 mrna]
Evidence
Data Source
Page of 19

15 Biological Test Results

15.1 BioAssay Results

348 items
Page of 70

16 Taxonomy

16 items
Page of 4

17 Classification

17.1 MeSH Tree

  • found in Gardenia jasminoides fruit; geniposide is the glycoside; structure; used as crosslinking agent (ADHESIVES)
    MeSH Concept: M0051258
    MeSH Descriptor: C007834

17.2 ChEBI Ontology

17.3 LIPID MAPS Classification

  • C10 isoprenoids (monoterpenes) [PR0102]

17.4 KEGG: Phytochemical Compounds

17.5 ChemIDplus

  • CTD
    Comparative Toxicogenomics Database - CTD selects and organizes gene, sequence, chemical, reference, and taxonomic data about gene-chemical interactions. It is hosted at North Carolina State University (NCSU).
  • ChEBI
    Chemical Entities of Biological Interest - Dictionary of molecular entities focused on "small" chemical compounds. ChEBI is part of the EMBL-European Bioinformatics Institute.
  • Cholagogues and Choleretics
  • DrugPortal
    Drug Information Portal - Portal to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies
  • EPA CompTox
Page of 4

17.6 ChEMBL Target Tree

  • Surface antigen
    Antigens on surfaces of cells, including infectious or foreign cells or viruses. They are usually protein-containing groups on cell membranes or walls and may be isolated. [MESH:D000954]
  • Transcription factor
    Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process. [MESH:D014157]
  • Tyrosine protein phosphatase
  • Transferase
    A group of enzymes that catalyze the transfer of a functional group from one molecule to another
  • HDAC class IIb

17.7 UN GHS Classification

  • H301: Toxic if swallowed [Danger: Acute toxicity, oral]
  • Acute toxicity, oral
  • GHS06: Acute Toxicity GHS06
  • P264: Wash hands [and ...] thoroughly after handling.
  • P270: Do not eat, drink or smoke when using this product.
Page of 2

17.8 NORMAN Suspect List Exchange Classification

  • List of compounds on the mzCloud mass spectral database (https://www.mzcloud.org/), provided by Robert Mistrik, update by Nikiforos Alygizakis. Dataset DOI:10.5281/zenodo.2628860
  • A list of NORMAN contributions to MassBank.EU (www.massbank.eu), typically processed with RMassBank (Stravs et al. 2013, DOI:10.1002/jms.3131). Dataset DOI:10.5281/zenodo.2621390
  • A merged list of >100,000 structures from the NORMAN Network Suspect List Exchange, available from https://www.norman-network.com/nds/susdat/. Compiled by Reza Aalizadeh, University of Athens, including RTI and toxicity values, support by Nikiforos Alygizakis, EI. Hazard and Exposure values provided by Stellan Fischer, KEMI. Dataset DOI:10.5281/zenodo.2664077

17.9 EPA DSSTox Classification

Page of 3

17.10 LOTUS: Biological Tree

  • Garrya elliptica
  • Gardenia jasminoides
  • Caenorhabditis elegans
  • Huito
  • Gardenia
Page of 2

17.11 LOTUS: Chemical Tree

  • Iridoids monoterpenoids

17.12 EPA Substance Registry Services Tree

  • Ecotoxicology Database
    ECOTOX :: Comprehensive database providing adverse effects of single chemical stressors to ecologically relevent aquatic and terrestrial species.
  • Chemical Abstracts Service Registry
    CAS Registry :: The CAS Registry database is the original supplier and final authority for CAS Registry Numbers (CASRNs or CAS Numbers). The Registry is updated daily. SRS uses this information resource to verify and identify former CAS Registry Numbers. There are no substance names associated with the CAS Registry acronym in SRS. Names obtained from Chemical Abstracts Service (CAS) are associated with the acronym for the specific Collective Index nomenclature rules that were used to assign the systematic name of the substance.

17.13 MolGenie Organic Chemistry Ontology

  • dialkyl ethers
  • chiral compounds
    Compounds that cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes.
  • cyclic compounds
    compounds containing at least one ring.
  • hydrophilic compounds
    Using a Fragment Based LogP value from OpenChemLib < 0
  • diols
Page of 8

17.14 Chemicals in PubChem from Regulatory Sources

  • Registered substancesunder REACH - there is an obligation on registrants to provide information on the substances they manufacture or import.

18 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
  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. ChEBI
  8. 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/
  9. 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
  10. Open Targets
    LICENSE
    Datasets generated by the Open Targets Platform are freely available for download.
    https://platform-docs.opentargets.org/licence
  11. 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
  12. 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
  13. Drug Gene Interaction database (DGIdb)
    LICENSE
    The data used in DGIdb is all open access and where possible made available as raw data dumps in the downloads section.
    http://www.dgidb.org/downloads
  14. Japan Chemical Substance Dictionary (Nikkaji)
  15. 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
  16. KNApSAcK Species-Metabolite Database
  17. Natural Product Activity and Species Source (NPASS)
  18. LIPID MAPS
    Lipid Classification
    https://www.lipidmaps.org/
  19. MassBank Europe
  20. 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
  21. SpectraBase
  22. Metabolomics Workbench
  23. NIAID ChemDB
    LICENSE
    The NIAID ChemDB information received cannot be sold and is only to be used for research purposes.
    methyl (1R,4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-1,4a,5,7a-tetrahydrocyclopenta[c]pyran-4-carboxylate
    https://pubchem.ncbi.nlm.nih.gov/substance/?source=niaid&sourceid=498531
    methyl (1R,4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-1,4a,5,7a-tetrahydrocyclopenta[c]pyran-4-carboxylate
    https://pubchem.ncbi.nlm.nih.gov/substance/?source=niaid&sourceid=498550
  24. Springer Nature
  25. Wikidata
  26. Wikipedia
  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. PubChem
    Chemicals in PubChem from Regulatory Sources
  29. GHS Classification (UNECE)
    GHS Classification
    https://unece.org/about-ghs
  30. 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/
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  31. EPA Substance Registry Services
    EPA SRS List Classification
    https://maldi.nist.gov
  32. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  33. PATENTSCOPE (WIPO)
  34. NCBI
CONTENTS