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Sphingosine

Athanor · official

C18H37NO2 · 299.5 g/mol

IUPAC name: (E,2S,3R)-2-aminooctadec-4-ene-1,3-diol

Also called sphingoid base, ceramide backbone

Lipids
Open in Athanor
The structure of Sphingosine
Drawn from its SMILES with RDKit
Harmful or irritantWarningCauses skin irritation · Causes serious eye irritation · May cause respiratory irritation

Names and identifiers

IUPAC name
(E,2S,3R)-2-aminooctadec-4-ene-1,3-diol
Synonyms
sphingoid base, ceramide backbone, D-erythro-Sphingosine
+ 37 more

D-Sphingosine, 4-Sphingenine, Sphingenine, (4E)-Sphingenine, (2S,3R,4E)-2-Amino-4-octadecene-1,3-diol, 4-trans-Sphingenine, (E,2S,3R)-2-aminooctadec-4-ene-1,3-diol, (2S,3R)-2-aminooctadec-4-ene-1,3-diol, (E)-2-Amino-4-octadecan-1,3-diol, NGZ37HRE42, CHEBI:16393, DTXSID90861763, (4E)-sphing-4-enine, 4-Octadecene-1,3-diol, 2-amino-, (R-(R*,S*-(E)))-, 2-amino-4-octadecene-1,3-diol, 4 Sphingenine, 4-Octadecene-1,3-diol, 2-amino-, [R-[R*,S*-(E)]]-, RefChem:888507, CHEBI:26738, DTXCID301436146, 204-651-3, Sphing-4-enine, (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol, trans-D-erythro-2-Amino-4-octadecene-1,3-diol, trans-4-Sphingenine, D-erythro-Sphingosine (synthetic), C18-Sphingosine, MFCD00036751, D-erythro-C18-Sphingosine, erythro-4-Sphingenine, dl-Erythro-sphingosine, Erythro-dl-sphingosine, 4-octadecene-1,3-diol, 2-amino-, (2S,3R,4E)-, Sphingoid, c18-erythro-sphingenine, (2S,3R)-Sphingosine, (-)-D-erythro-Sphingosine

Molecular formula
C18H37NO2
Empirical formula
C18H37NO2
Molecular weight
299.5 g/mol
Exact mass
299.28243
CAS number
123-78-4
PubChem CID
5280335
Canonical SMILES
CCCCCCCCCCCCCC=CC(C(CO)N)O
Isomeric SMILES
CCCCCCCCCCCCC/C=C/[C@H]([C@H](CO)N)O
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
InChIKey
WWUZIQQURGPMPG-KRWOKUGFSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms
21
Rings
0
Aromatic rings
0
Fraction sp³ carbons (Fsp3)
0.89
H-bond donors
3
H-bond acceptors
3
Rotatable bonds
15
TPSA (Ų)
66.5
Formal charge
0
XLogP3
5.3 PubChem
Complexity
231 PubChem
Stereocenters
2 definedCIP: C16: R · C18: S
Double-bond geometry
C14=C15: E
Point group
C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

  • C72.19%
  • H12.45%
  • N4.68%
  • O10.68%

Isotope pattern

100%299.28220%300.2862.4%301.289302.291

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P
3.92 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-3.18 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
3.09 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 299.5
  • log P ≤ 5 (Crippen): 3.92
  • H-bond donors ≤ 5: 3
  • H-bond acceptors ≤ 10: 3

Passes all four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

Warning

Most widely reported: 30 company reports to ECHA. Source [1].

  • Harmful or irritant
  • H315Causes skin irritation (96.7% of reports)
  • H319Causes serious eye irritation (96.7% of reports)
  • H335May cause respiratory irritation (96.7% of reports)

Precautionary statements: P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, P501

View all classifications (2)
  • [1] European Chemicals Agency (ECHA)This chemical does not meet GHS hazard criteria for 3.3% (1 of 30) of reports.
  • [1] European Chemicals Agency (ECHA) · 30 reports · WarningH315, H319, H335

Safety data sheets on the supplier’s page: LGC Standards, Sigma-Aldrich, Excenen Pharmatech.

Always read the supplier’s safety data sheet before working with it.

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. [1]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
  2. [2]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
  3. [3]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
  4. [4]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
  5. [5]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
  6. [6]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
  7. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  8. ·Literature on PubChem

Data last updated 2026-10-14.