An official website of the United States government

Sphingosine

PubChem CID
5280335
Structure
Sphingosine_small.png
Sphingosine_3D_Structure.png
Molecular Formula
Synonyms
  • sphingosine
  • D-erythro-Sphingosine
  • 123-78-4
  • D-Sphingosine
  • 4-Sphingenine
Molecular Weight
299.5 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-18
Description
Sphingosine is a sphing-4-enine in which the double bond is trans. It has a role as a human metabolite and a mouse metabolite. It is a conjugate base of a sphingosine(1+). It is an enantiomer of a L-erythro-sphingosine.
An amino alcohol with a long unsaturated hydrocarbon chain. Sphingosine and its derivative sphinganine are the major bases of the sphingolipids in mammals. (Dorland, 28th ed)
Sphingosine has been reported in Rehmannia glutinosa, Glycine max, and other organisms with data available.
See also: L-erythro-Sphingosine (annotation moved to).

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Sphingosine.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

(E,2S,3R)-2-aminooctadec-4-ene-1,3-diol
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h14-15,17-18,20-21H,2-13,16,19H2,1H3/b15-14+/t17-,18+/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

WWUZIQQURGPMPG-KRWOKUGFSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

CCCCCCCCCCCCC/C=C/[C@H]([C@H](CO)N)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C18H37NO2
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

2733-29-1

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 Lipid Maps ID (LM_ID)

2.3.11 Metabolomics Workbench ID

2.3.12 Nikkaji Number

2.3.13 Pharos Ligand ID

2.3.14 Wikidata

2.3.15 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • 4 Sphingenine
  • 4-Sphingenine
  • Sphingosine

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
299.5 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
5.3
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
15
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
299.282429423 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
299.282429423 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
66.5 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
21
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
231
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
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
1
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 Experimental Properties

3.2.1 Physical Description

Solid

3.2.2 Melting Point

67 °C
PhysProp
81 °C

3.2.3 Collision Cross Section

186 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]

3.3 Chemical Classes

3.3.1 Drugs

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

3.3.2 Lipids

Lipids -> Sphingolipids [SP] -> Sphingoid bases [SP01] -> Sphing-4-enines (Sphingosines) [SP0101]

4 Spectral Information

4.1 1D NMR Spectra

4.1.1 1H NMR Spectra

Spectra ID
Instrument Type
Bruker
Frequency
600 MHz
Solvent
CD3OD
pH
7.00
Shifts [ppm]:Intensity
5.51:1.61, 5.71:1.85, 2.75:4.29, 3.95:3.26, 3.96:5.39, 2.74:3.89, 1.40:4.63, 5.72:3.72, 0.88:11.23, 3.65:5.94, 3.50:4.99, 5.50:1.81, 2.07:7.24, 5.75:1.12, 2.08:6.97, 1.39:2.05, 1.42:3.23, 2.06:2.89, 1.29:100.00, 5.51:3.35, 5.74:2.64, 5.47:1.39, 3.97:3.24, 3.47:4.64, 2.10:2.59, 1.41:5.35, 5.51:2.35, 2.74:4.18, 0.90:23.91, 5.49:1.39, 3.68:4.37, 5.74:3.05, 1.43:0.93, 5.50:3.54, 5.75:1.36, 2.76:2.47, 3.48:4.66, 1.31:18.76, 5.48:2.72, 1.32:10.57, 2.75:3.59, 5.73:2.23, 1.33:6.32, 5.47:2.74, 3.67:5.34, 2.74:3.76, 5.73:2.38, 5.49:2.43, 5.48:1.97, 2.73:2.59, 3.66:5.58, 5.47:1.97, 5.71:1.66, 0.91:9.27, 3.49:5.78, 5.72:3.27, 2.75:3.09
Thumbnail
Thumbnail

4.1.2 13C NMR Spectra

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

4.2 2D NMR Spectra

4.2.1 1H-13C NMR Spectra

2D NMR Spectra Type
1H-13C HSQC
Spectra ID
Instrument Type
Bruker
Frequency
600 MHz
Solvent
CD3OD
pH
7.00
Shifts [ppm] (F2:F1):Intensity
1.34:30.24:0.04, 3.96:75.04:0.15, 0.90:14.28:0.02, 2.08:33.37:0.15, 5.73:135.12:0.05, 1.29:30.71:1.00, 5.49:130.80:0.05, 1.30:23.57:0.04, 2.75:57.94:0.12, 3.49:64.41:0.09, 1.28:32.87:0.09, 1.41:30.34:0.12, 3.67:64.41:0.07
Thumbnail
Thumbnail

4.3 Mass Spectrometry

4.3.1 GC-MS

1 of 6
View All
Spectra ID
Instrument Type
GC-MS
Top 5 Peaks

204.0 1

205.0 0.22

100.0 0.12

206.0 0.10

116.0 0.10

Thumbnail
Thumbnail
2 of 6
View All
Spectra ID
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

204.0 100

205.0 17.52

147.0 9.11

100.0 9.11

206.0 7.71

Thumbnail
Thumbnail
Notes
instrument=Leco Pegasus IV

4.3.2 MS-MS

1 of 7
View All
Spectra ID
Ionization Mode
Positive
Top 5 Peaks

282.2773 100

300.2875 18.73

299.3479 2.35

Thumbnail
Thumbnail
2 of 7
View All
Spectra ID
Ionization Mode
Positive
Top 5 Peaks

93.0692 100

95.085 99.16

83.0484 46.27

91.0536 45.08

96.0804 40.04

Thumbnail
Thumbnail

4.3.3 LC-MS

1 of 7
View All
Authors
BGC, Helmholtz Zentrum Muenchen
Instrument
maXis plus UHR-ToF-MS, Bruker Daltonics
Instrument Type
LC-ESI-QTOF
MS Level
MS2
Ionization Mode
POSITIVE
Ionization
ESI
Collision Energy
10
Fragmentation Mode
CID
Column Name
BEH C18 1.7um, 2.1x100mm, Waters
Retention Time
5.325 min
Precursor m/z
300.2897
Precursor Adduct
[M+H]+
Top 5 Peaks

282.2787 999

300.2892 262

283.2821 213

252.2681 14

211.205 13

Thumbnail
Thumbnail
License
CC BY
2 of 7
View All
Authors
BGC, Helmholtz Zentrum Muenchen
Instrument
maXis plus UHR-ToF-MS, Bruker Daltonics
Instrument Type
LC-ESI-QTOF
MS Level
MS2
Ionization Mode
POSITIVE
Ionization
ESI
Collision Energy
20
Fragmentation Mode
CID
Column Name
BEH C18 1.7um, 2.1x100mm, Waters
Retention Time
5.325 min
Precursor m/z
300.2897
Precursor Adduct
[M+H]+
Top 5 Peaks

282.2787 999

283.2822 246

252.2682 163

264.2682 104

95.0846 82

Thumbnail
Thumbnail
License
CC BY

4.3.4 Other MS

MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
300.29
Instrument
Orbitrap
Ionization Mode
positive
Top 5 Peaks

282.304718 100

252.290863 20.26

264.293579 13.05

56.050301 5.42

81.071899 5.02

Thumbnail
Thumbnail

6 Chemical Vendors

7 Food Additives and Ingredients

7.1 Associated Foods

8 Pharmacology and Biochemistry

8.1 Human Metabolite Information

8.1.1 Tissue Locations

  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Leukocyte
  • Liver
  • Placenta
  • Platelet
  • Skeletal Muscle
  • Spleen

8.1.2 Cellular Locations

  • Cytoplasm
  • Endoplasmic reticulum
  • Extracellular
  • Lysosome
  • Membrane

8.1.3 Metabolite Pathways

8.2 Biochemical Reactions

9 Safety and Hazards

9.1 Hazards Identification

9.1.1 GHS Classification

Note
Pictograms displayed are for 96.7% (29 of 30) of reports that indicate hazard statements. This chemical does not meet GHS hazard criteria for 3.3% (1 of 30) of reports.
Pictogram(s)
Irritant
Signal
Warning
GHS Hazard Statements

H315 (96.7%): Causes skin irritation [Warning Skin corrosion/irritation]

H319 (96.7%): Causes serious eye irritation [Warning Serious eye damage/eye irritation]

H335 (96.7%): May cause respiratory irritation [Warning Specific target organ toxicity, single exposure; Respiratory tract irritation]

Precautionary Statement Codes

P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, 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 30 reports by companies from 3 notifications to the ECHA C&L Inventory. Each notification may be associated with multiple companies.

Reported as not meeting GHS hazard criteria per 1 of 30 reports by companies. For more detailed information, please visit ECHA C&L website.

There are 2 notifications provided by 29 of 30 reports by companies with hazard statement code(s).

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.

9.1.2 Hazard Classes and Categories

Skin Irrit. 2 (96.7%)

Eye Irrit. 2 (96.7%)

STOT SE 3 (96.7%)

10 Associated Disorders and Diseases

Disease
Lung Cancer
References
Disease
Colorectal cancer
References

PubMed: 7482520, 19006102, 23940645, 24424155, 20156336, 19678709, 22148915, 25105552, 21773981, 25037050, 27015276, 27107423, 27275383, 28587349

Silke Matysik, Caroline Ivanne Le Roy, Gerhard Liebisch, Sandrine Paule Claus. Metabolomics of fecal samples: A practical consideration. Trends in Food Science & Technology. Vol. 57, Part B, Nov. 2016, p.244-255: http://www.sciencedirect.com/science/article/pii/S0924224416301984

11 Literature

11.1 Consolidated References

11.2 NLM Curated PubMed Citations

11.3 Springer Nature References

11.4 Thieme References

11.5 Nature Journal References

11.6 Chemical Co-Occurrences in Literature

11.7 Chemical-Gene Co-Occurrences in Literature

11.8 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

WormJam Metabolites Local CSV for MetFrag | DOI:10.5281/zenodo.3403364
WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series, Worm, 6:2, e1373939, DOI:10.1080/21624054.2017.1373939
Zebrafish Pathway Metabolite MetFrag Local CSV (Beta) | DOI:10.5281/zenodo.3457553
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 ChEBI Ontology

16.3 LIPID MAPS Classification

16.4 KEGG: Lipid

16.5 ChemIDplus

16.6 IUPHAR / BPS Guide to PHARMACOLOGY Target Classification

16.7 ChEMBL Target Tree

16.8 UN GHS Classification

16.9 NORMAN Suspect List Exchange Classification

16.10 CCSBase Classification

16.11 EPA DSSTox Classification

16.12 LOTUS Tree

16.13 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
  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. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  9. ChEBI
  10. 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/
  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. 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. IUPHAR/BPS Guide to PHARMACOLOGY
    LICENSE
    The Guide to PHARMACOLOGY database is licensed under the Open Data Commons Open Database License (ODbL) https://opendatacommons.org/licenses/odbl/. Its contents are licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (http://creativecommons.org/licenses/by-sa/4.0/)
    https://www.guidetopharmacology.org/about.jsp#license
    Guide to Pharmacology Target Classification
    https://www.guidetopharmacology.org/targets.jsp
  15. Therapeutic Target Database (TTD)
  16. ECI Group, LCSB, University of Luxembourg
    LICENSE
    Data: CC-BY 4.0; Code: Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    sphingosine
  17. KNApSAcK Species-Metabolite Database
  18. Natural Product Activity and Species Source (NPASS)
  19. 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
  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
    [2S,3R,(4E)]-2-AMINOOCTADEC-4-ENE-1,3-DIOL;(-)-D-ERYTHRO-SPHINGOSINE
    https://spectrabase.com/spectrum/9Yao9oFDoKr
  22. NIST Mass Spectrometry Data Center
    LICENSE
    Data covered by the Standard Reference Data Act of 1968 as amended.
    https://www.nist.gov/srd/public-law
    D-erythro-C18-Sphingosine
    http://www.nist.gov/srd/nist1a.cfm
  23. Japan Chemical Substance Dictionary (Nikkaji)
  24. 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
  25. LIPID MAPS
    Lipid Classification
    https://www.lipidmaps.org/
  26. MassBank Europe
  27. Metabolomics Workbench
  28. Nature Chemical Biology
  29. 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/
    Sphingosine
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  30. Pharos
    LICENSE
    Data accessed from Pharos and TCRD is publicly available from the primary sources listed above. Please respect their individual licenses regarding proper use and redistribution.
    https://pharos.nih.gov/about
  31. Protein Data Bank in Europe (PDBe)
  32. 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
  33. Springer Nature
  34. 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/
  35. Wikidata
  36. Wikipedia
  37. 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
  38. PubChem
  39. GHS Classification (UNECE)
  40. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  41. PATENTSCOPE (WIPO)
CONTENTS