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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2020-06-10 19:12:20 UTC
Update Date2022-11-30 19:53:43 UTC
HMDB IDHMDB0240672
Secondary Accession NumbersNone
Metabolite Identification
Common NameSM(d16:1/24:2(5Z,9Z))
DescriptionSphingomyelin (d16:1/24:2(5Z,9Z)) or SM(d16:1/24:2(5Z,9Z)) is a type of sphingolipid found in animal cell membranes, especially in the membranous myelin sheath which surrounds some nerve cell axons. It usually consists of phosphorylcholine and ceramide. SM(d16:1/24:2(5Z,9Z)) consists of a hexadecasphingosine backbone and a 5Z,9Z-tetracosadienoic acid chain. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. Like all sphingolipids, SM has a ceramide core (sphingosine bonded to a fatty acid via an amide linkage). In addition, it contains one polar head group, which is either phosphocholine or phosphoethanolamine. The plasma membrane of cells is highly enriched in sphingomyelin and is considered largely to be found in the exoplasmic leaflet of the cell membrane. However, there is some evidence that there may also be a sphingomyelin pool in the inner leaflet of the membrane. Moreover, neutral sphingomyelinase-2, an enzyme that breaks down sphingomyelin into ceramide, has been found to localize exclusively to the inner leaflet further suggesting that there may be sphingomyelin present there. Sphingomyelin can accumulate in a rare hereditary disease called Niemann-Pick Disease, types A and B. Niemann-Pick disease is a genetically-inherited disease caused by a deficiency in the enzyme sphingomyelinase, which causes the accumulation of sphingomyelin in spleen, liver, lungs, bone marrow, and the brain, causing irreversible neurological damage. SMs play a role in signal transduction. Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.
Structure
Data?1591817173
Synonyms
ValueSource
SM D16:1/24:2HMDB
SM D16:1/24:2(5Z,9Z)HMDB
SM(D16:1/24:2)HMDB
Sphingomyelin (D16:1,C24:2)HMDB
Sphingomyelin (D16:1,C24:2(5Z,9Z))HMDB
Sphingomyelin (D16:1/24:2(5Z,9Z))HMDB
Sphingomyelin (D16:1/24:2)HMDB
SM(d16:1/24:2(5Z,9Z))HMDB
Chemical FormulaC45H87N2O6P
Average Molecular Weight783.173
Monoisotopic Molecular Weight782.630175527
IUPAC Name(2-{[(2S,3R,4E)-3-hydroxy-2-[(5Z,9Z)-tetracosa-5,9-dienamido]hexadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E)-3-hydroxy-2-[(5Z,9Z)-tetracosa-5,9-dienamido]hexadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCC\C=C/CC\C=C/CCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCC
InChI Identifier
InChI=1S/C45H87N2O6P/c1-6-8-10-12-14-16-18-19-20-21-22-23-24-25-26-27-29-31-33-35-37-39-45(49)46-43(42-53-54(50,51)52-41-40-47(3,4)5)44(48)38-36-34-32-30-28-17-15-13-11-9-7-2/h25-26,31,33,36,38,43-44,48H,6-24,27-30,32,34-35,37,39-42H2,1-5H3,(H-,46,49,50,51)/b26-25-,33-31-,38-36+/t43-,44+/m0/s1
InChI KeyUBIHPQPZTXWSQU-VDXRCOLOSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphocholines. Phosphocholines are compounds containing a [2-(trimethylazaniumyl)ethoxy]phosphonic acid or derivative.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassQuaternary ammonium salts
Direct ParentPhosphocholines
Alternative Parents
Substituents
  • Phosphocholine
  • Dialkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetraalkylammonium salt
  • Secondary alcohol
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organic zwitterion
  • Organooxygen compound
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Disposition
Process
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP6.07ALOGPS
logP8.92ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area107.92 ŲChemAxon
Rotatable Bond Count40ChemAxon
Refractivity243.78 m³·mol⁻¹ChemAxon
Polarizability98.24 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+288.30230932474
DeepCCS[M-H]-285.90730932474
DeepCCS[M-2H]-318.95830932474
DeepCCS[M+Na]+294.07230932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
SM(d16:1/24:2(5Z,9Z))[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCC\C=C/CC\C=C/CCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCC5111.3Standard polar33892256
SM(d16:1/24:2(5Z,9Z))[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCC\C=C/CC\C=C/CCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCC4136.0Standard non polar33892256
SM(d16:1/24:2(5Z,9Z))[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCC\C=C/CC\C=C/CCCCCCCCCCCCCC)[C@H](O)\C=C\CCCCCCCCCCC5472.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - SM(d16:1/24:2(5Z,9Z)) GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d16:1/24:2(5Z,9Z)) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d16:1/24:2(5Z,9Z)) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d16:1/24:2(5Z,9Z)) GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 10V, Positive-QTOFsplash10-0a4i-0000001190-6ef73f6d11ce1a7c9a8c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 20V, Positive-QTOFsplash10-0ai0-0000009290-f12fe1df9dac5c0907f02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 40V, Positive-QTOFsplash10-00di-0000019110-40275fd5a0c028ad2d222021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 10V, Positive-QTOFsplash10-000i-0000001900-85c8beea315647e763282021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 20V, Positive-QTOFsplash10-0a50-0000007900-56169e1eb34ee831c7c12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 40V, Positive-QTOFsplash10-0a4i-0000019200-62eb63aefd784c627ffa2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 10V, Positive-QTOFsplash10-001i-0600000900-3d085ad7b140d8040ce32021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 20V, Positive-QTOFsplash10-001i-0600000900-3d085ad7b140d8040ce32021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 40V, Positive-QTOFsplash10-001i-0900000300-986cdd39846b933d16792021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 10V, Negative-QTOFsplash10-001i-0000000900-67051d4a4600d6c73e212021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 20V, Negative-QTOFsplash10-001i-1000003900-9e3a96b2807cec56b6c82021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/24:2(5Z,9Z)) 40V, Negative-QTOFsplash10-004i-9000000000-5c6eb18861fe496150b92021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available