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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2019-12-18 18:37:11 UTC
Update Date2023-07-07 20:54:00 UTC
HMDB IDHMDB0240613
Secondary Accession NumbersNone
Metabolite Identification
Common NameSM(d18:1/16:1)
DescriptionSphingomyelin (d18:1/16:1(9Z)) or SM(d18:1/16:1(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(d18:1/16:1(9Z)) consists of a sphingosine backbone and a palmitoleic 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?1576694518
Synonyms
ValueSource
N-(9Z-Hexadecenoyl)-sphing-4-enine-1-phosphocholineChEBI
SM(34:2)ChEBI
SM(D18:1/16:1)ChEBI
SphingomyelinMetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-sphing-4-enineMetBuilder
Sphingomyelin(D18:1/16:1(9Z))MetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-sphingosineMetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-D-erythro-sphingosineMetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-4-sphingenineMetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-D-sphingosineMetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-sphingenineMetBuilder
N-(9Z-Hexadecenoyl)-1-phosphocholine-erythro-4-sphingenineMetBuilder
SM d18:1/16:1(9Z)HMDB
SM(d18:1/16:1(9Z))HMDB
Sphingomyelin (d18:1,C16:1(9Z))HMDB
Sphingomyelin (d18:1/16:1(9Z))HMDB
Chemical FormulaC39H77N2O6P
Average Molecular Weight701.027
Monoisotopic Molecular Weight700.551925205
IUPAC Name(2-{[(2S,3R,4E)-2-[(9Z)-hexadec-9-enamido]-3-hydroxyoctadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E)-2-[(9Z)-hexadec-9-enamido]-3-hydroxyoctadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
CAS Registry Number222403-66-9
SMILES
[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCC\C=C/CCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC
InChI Identifier
InChI=1S/C39H77N2O6P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-38(42)37(36-47-48(44,45)46-35-34-41(3,4)5)40-39(43)33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h17,19,30,32,37-38,42H,6-16,18,20-29,31,33-36H2,1-5H3,(H-,40,43,44,45)/b19-17-,32-30+/t37-,38+/m0/s1
InChI KeyOAHFTKWSJGVMTG-MBIABJCFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassPhosphosphingolipids
Direct ParentPhosphosphingolipids
Alternative Parents
Substituents
  • Sphingoid-1-phosphate or derivatives
  • Phosphocholine
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Fatty amide
  • N-acyl-amine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Fatty acyl
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Carboxylic acid derivative
  • Organic zwitterion
  • Alcohol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Amine
  • Organic salt
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
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
logP5.04ALOGPS
logP6.61ChemAxon
logS-7.4ALOGPS
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 Count35ChemAxon
Refractivity215.06 m³·mol⁻¹ChemAxon
Polarizability86.35 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]+280.47430932474
DeepCCS[M-H]-278.3930932474
DeepCCS[M-2H]-311.63130932474
DeepCCS[M+Na]+286.38730932474
AllCCS[M+H]+280.632859911
AllCCS[M+H-H2O]+280.332859911
AllCCS[M+NH4]+280.932859911
AllCCS[M+Na]+280.932859911
AllCCS[M-H]-270.732859911
AllCCS[M+Na-2H]-275.032859911
AllCCS[M+HCOO]-279.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
SM(d18:1/16:1(9Z))[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCC\C=C/CCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC4689.8Standard polar33892256
SM(d18:1/16:1(9Z))[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCC\C=C/CCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC3878.0Standard non polar33892256
SM(d18:1/16:1(9Z))[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCC\C=C/CCCCCC)[C@H](O)\C=C\CCCCCCCCCCCCC4869.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
SM(d18:1/16:1(9Z)),2TMS,isomer #1CCCCCC/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4692.6Semi standard non polar33892256
SM(d18:1/16:1(9Z)),2TMS,isomer #1CCCCCC/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4453.4Standard non polar33892256
SM(d18:1/16:1(9Z)),2TMS,isomer #1CCCCCC/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C5180.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:1/16:1) GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:1/16:1) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:1/16:1) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:1/16:1) 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(d18:1/16:1) 10V, Negative-QTOFsplash10-0002-0000009000-14c06d7026f68e46e7172021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 20V, Negative-QTOFsplash10-0002-1000019000-4ed3961bcdefeeff8be32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 40V, Negative-QTOFsplash10-004i-9000000000-4d469800c401018d13f32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 10V, Positive-QTOFsplash10-0a4i-0000011900-0b6f839bb507e84e2d372021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 20V, Positive-QTOFsplash10-0ai0-0000092900-c70356bb9ee72c47ab052021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 40V, Positive-QTOFsplash10-00di-0000091100-c5f2a4aa6139afa051a12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 10V, Positive-QTOFsplash10-0ue9-0600000900-8c5994c520166ad0168a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 20V, Positive-QTOFsplash10-0ue9-0600000900-8c5994c520166ad0168a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 40V, Positive-QTOFsplash10-001i-0900001100-4758c2069a17dd9917882021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 10V, Positive-QTOFsplash10-00di-0000011900-ec110f63d6ad5a5ee14c2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 20V, Positive-QTOFsplash10-00do-0000092900-cc59983338e7dfd1cb852021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:1/16:1) 40V, Positive-QTOFsplash10-0006-0000091100-b4adf128e096ec9238562021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue Locations
  • Placenta
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 ID34448430
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID64487
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 References
  1. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]