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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2009-03-24 16:22:11 UTC
Update Date2022-03-07 02:51:20 UTC
HMDB IDHMDB0012089
Secondary Accession Numbers
  • HMDB12089
Metabolite Identification
Common NameSM(d18:0/18:1(9Z))
DescriptionSphingomyelin (d18:0/18:1(9Z)) or SM(d18:0/18:1(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. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. Like all sphingolipids, SPH 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 localise 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?1582753010
Synonyms
ValueSource
(2-{[(2S,3R)-3-hydroxy-2-[(9Z)-octadec-9-enamido]octadecyl phosphonato]oxy}ethyl)trimethylazaniumChEBI
C18:1DH SphingomyelinChEBI
N-(9Z-Octadecenoyl)-sphinganine-1-phosphocholineChEBI
N-[(9Z)-Octadecenoyl]dihydrsphingosine-1-phosphocholineChEBI
N-[(9Z)-Octadecenoyl]sphinganine-1-phosphocholineChEBI
Sphingomyelin (D18:0/18:1(9Z))ChEBI
SphingomyelinHMDB
N-(9Z-Octadecenoyl)-1-phosphocholine-sphinganineHMDB
Sphingomyelin(D18:0/18:1(9Z))HMDB
N-(9Z-Octadecenoyl)-1-phosphocholine-dihydrosphingosineHMDB
N-(9Z-Octadecenoyl)-1-phosphocholine-D-erythro-sphinganineHMDB
SM(D18:0/18:1(9Z))ChEBI
Chemical FormulaC41H83N2O6P
Average Molecular Weight731.0813
Monoisotopic Molecular Weight730.59887491
IUPAC Name(2-{[(2S,3R)-3-hydroxy-2-[(9Z)-octadec-9-enamido]octadecyl phosphonato]oxy}ethyl)trimethylazanium
Traditional NameC18:1DH sphingomyelin
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCC[C@@H](O)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)NC(=O)CCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C41H83N2O6P/c1-6-8-10-12-14-16-18-20-21-23-25-27-29-31-33-35-41(45)42-39(38-49-50(46,47)48-37-36-43(3,4)5)40(44)34-32-30-28-26-24-22-19-17-15-13-11-9-7-2/h20-21,39-40,44H,6-19,22-38H2,1-5H3,(H-,42,45,46,47)/b21-20-/t39-,40+/m0/s1
InChI KeyXYLWKHKCYHMVMA-RVPJYPCXSA-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
Not AvailableNot Available
Physical Properties
StateSolid
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
Water Solubility3.2e-05 g/LALOGPS
logP5.41ALOGPS
logP8.8ChemAxon
logS-7.4ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.025ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area107.92 ŲChemAxon
Rotatable Bond Count38ChemAxon
Refractivity223.3 m³·mol⁻¹ChemAxon
Polarizability92.66 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]+286.80130932474
DeepCCS[M-H]-284.90530932474
DeepCCS[M-2H]-318.14330932474
DeepCCS[M+Na]+292.51130932474
AllCCS[M+H]+290.232859911
AllCCS[M+H-H2O]+290.032859911
AllCCS[M+NH4]+290.332859911
AllCCS[M+Na]+290.432859911
AllCCS[M-H]-281.832859911
AllCCS[M+Na-2H]-285.632859911
AllCCS[M+HCOO]-289.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
SM(d18:0/18:1(9Z))CCCCCCCCCCCCCCC[C@@H](O)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)NC(=O)CCCCCCC\C=C/CCCCCCCC4760.6Standard polar33892256
SM(d18:0/18:1(9Z))CCCCCCCCCCCCCCC[C@@H](O)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)NC(=O)CCCCCCC\C=C/CCCCCCCC4088.3Standard non polar33892256
SM(d18:0/18:1(9Z))CCCCCCCCCCCCCCC[C@@H](O)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)NC(=O)CCCCCCC\C=C/CCCCCCCC5099.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
SM(d18:0/18:1(9Z)),2TMS,isomer #1CCCCCCCC/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](CCCCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4916.8Semi standard non polar33892256
SM(d18:0/18:1(9Z)),2TMS,isomer #1CCCCCCCC/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](CCCCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4681.4Standard non polar33892256
SM(d18:0/18:1(9Z)),2TMS,isomer #1CCCCCCCC/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](CCCCCCCCCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C5438.1Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:0/18:1(9Z)) GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:0/18:1(9Z)) GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:0/18:1(9Z)) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - SM(d18:0/18:1(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(d18:0/18:1(9Z)) 10V, Negative-QTOFsplash10-004i-0000000900-ccbe9989e1fd1bcbc5c22021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 20V, Negative-QTOFsplash10-004i-0000003900-59c738f3ab132aa95f002021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 40V, Negative-QTOFsplash10-004i-9010201000-14aa95bba7480ad7ca5e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 10V, Positive-QTOFsplash10-000i-0000011900-3c5bfe1569948d5a91632021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 20V, Positive-QTOFsplash10-0ue0-0000092900-22361e6fb4d808e61d7c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 40V, Positive-QTOFsplash10-0udi-0000091100-e540baeeed6b4bfc12e32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 10V, Positive-QTOFsplash10-001i-0600000900-3875b4498c76a7f087f12021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 20V, Positive-QTOFsplash10-001i-0600000900-3875b4498c76a7f087f12021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 40V, Positive-QTOFsplash10-001i-0900000300-7545f6efae8c805dfd032021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 10V, Positive-QTOFsplash10-0udi-0000011900-2e17d386a09bab10148a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 20V, Positive-QTOFsplash10-0ur0-0000092900-e017aa7fd289fad1a8bf2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d18:0/18:1(9Z)) 40V, Positive-QTOFsplash10-00di-0000091100-323c52a44d4be0c1b88d2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified11.0 +/- 2.56 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Not Specified
Premature neonates
details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028756
KNApSAcK IDNot Available
Chemspider ID24846887
KEGG Compound IDC00550
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44260139
PDB IDNot Available
ChEBI ID17636
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. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. Ghosh S, Strum JC, Bell RM: Lipid biochemistry: functions of glycerolipids and sphingolipids in cellular signaling. FASEB J. 1997 Jan;11(1):45-50. [PubMed:9034165 ]
  7. Hannun YA: The sphingomyelin cycle and the second messenger function of ceramide. J Biol Chem. 1994 Feb 4;269(5):3125-8. [PubMed:8106344 ]
  8. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  9. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Only showing the first 10 proteins. There are 50 proteins in total.

Enzymes

General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
General function:
Involved in hydrolase activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic activity.
Gene Name:
SMPD1
Uniprot ID:
P17405
Molecular weight:
69935.53
General function:
Involved in galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity
Specific function:
Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo-orosomucoid (ASOR), asialo-fetuin, and asialo-neural cell adhesion molecule. Requires sphingomyelin for activity: stearoyl-sphingomyelin was the most effective, followed by palmitoyl-sphingomyelin and lignoceroyl-sphingomyelin. Activity was demonstrated only for sphingomyelin with a saturated fatty acid and not for that with an unsaturated fatty acid, regardless of the length of the acyl group (By similarity).
Gene Name:
B3GAT1
Uniprot ID:
Q9P2W7
Molecular weight:
38255.675
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGP
Uniprot ID:
P57054
Molecular weight:
18089.055
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGC
Uniprot ID:
Q92535
Molecular weight:
33582.18
General function:
Involved in catalytic activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activity toward palmitoyl lyso-phosphocholine. Does not appear to have nucleotide pyrophosphatase activity.
Gene Name:
ENPP7
Uniprot ID:
Q6UWV6
Molecular weight:
51493.415

Only showing the first 10 proteins. There are 50 proteins in total.