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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 02:40:35 UTC
Update Date2022-11-30 20:07:05 UTC
HMDB IDHMDB0290278
Secondary Accession NumbersNone
Metabolite Identification
Common NameSM(d16:1/18:2(9Z,11E)+=O(13))
DescriptionSM(d16:1/18:2(9Z,11E)+=O(13)) is a type of oxidized sphingolipid found in animal cell membranes. It usually consists of phosphorylcholine and ceramide. SM(d16:1/18:2(9Z,11E)+=O(13)) consists of a sphingosine backbone and a 13-oxo-octadecadienoyl 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
Thumb
SynonymsNot Available
Chemical FormulaC39H73N2O7P
Average Molecular Weight712.994
Monoisotopic Molecular Weight712.515539697
IUPAC Name(2-{[(2S,3R,4E)-3-hydroxy-2-[(9Z,11E)-13-oxooctadeca-9,11-dienamido]hexadec-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E)-3-hydroxy-2-[(9Z,11E)-13-oxooctadeca-9,11-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)CCCCCCC\C=C/C=C/C(=O)CCCCC)[C@H](O)\C=C\CCCCCCCCCCC
InChI Identifier
InChI=1S/C39H73N2O7P/c1-6-8-10-11-12-13-14-17-20-23-27-31-38(43)37(35-48-49(45,46)47-34-33-41(3,4)5)40-39(44)32-28-24-21-18-15-16-19-22-26-30-36(42)29-25-9-7-2/h19,22,26-27,30-31,37-38,43H,6-18,20-21,23-25,28-29,32-35H2,1-5H3,(H-,40,44,45,46)/b22-19-,30-26+,31-27+/t37-,38+/m0/s1
InChI KeyVUSOFCBFZSOKRT-FVFOBAOISA-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
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • N-acyl-amine
  • Fatty amide
  • Tetraalkylammonium salt
  • Alpha,beta-unsaturated ketone
  • Enone
  • Acryloyl-group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Ketone
  • Carboxamide group
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organic zwitterion
  • Organooxygen compound
  • Carbonyl group
  • 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
logP4.31ALOGPS
logP5.43ChemAxon
logS-7.3ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area124.99 ŲChemAxon
Rotatable Bond Count34ChemAxon
Refractivity216.79 m³·mol⁻¹ChemAxon
Polarizability87.05 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
AllCCS[M+H]+279.25532859911
AllCCS[M+H-H2O]+278.95332859911
AllCCS[M+Na]+279.56932859911
AllCCS[M+NH4]+279.50332859911
AllCCS[M-H]-269.83132859911
AllCCS[M+Na-2H]-274.17432859911
AllCCS[M+HCOO]-278.98632859911
DeepCCS[M+H]+278.30630932474
DeepCCS[M-H]-275.95430932474
DeepCCS[M-2H]-309.19430932474
DeepCCS[M+Na]+284.17530932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. 8.11 minutes32390414
Predicted by Siyang on May 30, 202225.9979 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.6 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4395.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid192.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid322.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid195.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid779.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1302.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid947.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)607.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3111.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid933.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2675.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid772.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid664.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate152.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA152.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.0 seconds40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #1CCCCC=C(/C=C/C=C\CCCCCCCC(=O)N[C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CCCCCCCCCCC)O[Si](C)(C)C)O[Si](C)(C)C5042.5Semi standard non polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #1CCCCC=C(/C=C/C=C\CCCCCCCC(=O)N[C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CCCCCCCCCCC)O[Si](C)(C)C)O[Si](C)(C)C4612.6Standard non polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #1CCCCC=C(/C=C/C=C\CCCCCCCC(=O)N[C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CCCCCCCCCCC)O[Si](C)(C)C)O[Si](C)(C)C5600.9Standard polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #2CCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)N(C(=O)CCCCCCC/C=C\C=C\C(=O)CCCCC)[Si](C)(C)C4913.8Semi standard non polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #2CCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)N(C(=O)CCCCCCC/C=C\C=C\C(=O)CCCCC)[Si](C)(C)C4617.0Standard non polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #2CCCCCCCCCCC/C=C/[C@@H](O[Si](C)(C)C)[C@H](COP(=O)([O-])OCC[N+](C)(C)C)N(C(=O)CCCCCCC/C=C\C=C\C(=O)CCCCC)[Si](C)(C)C5479.6Standard polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #3CCCCC=C(/C=C/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCC)[Si](C)(C)C)O[Si](C)(C)C4977.7Semi standard non polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #3CCCCC=C(/C=C/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCC)[Si](C)(C)C)O[Si](C)(C)C4678.9Standard non polar33892256
SM(d16:1/18:2(9Z,11E)+=O(13)),2TMS,isomer #3CCCCC=C(/C=C/C=C\CCCCCCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@H](O)/C=C/CCCCCCCCCCC)[Si](C)(C)C)O[Si](C)(C)C5759.4Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 10V, Positive-QTOFsplash10-03e9-0600000900-eeaa2078ae256905bd562021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 20V, Positive-QTOFsplash10-03e9-0600000900-eeaa2078ae256905bd562021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 40V, Positive-QTOFsplash10-001i-0900001100-318d653bd5dffee0a61f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 10V, Positive-QTOFsplash10-014i-0000011900-1b6e74235eeebba24dec2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 20V, Positive-QTOFsplash10-0150-0000092900-7f0deba4144f4803f0762021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 40V, Positive-QTOFsplash10-000i-0000091100-66a39f1e71193d9a4df92021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 10V, Positive-QTOFsplash10-000i-0000011900-d075d3c903ac7e8e945f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 20V, Positive-QTOFsplash10-0ue0-0000092900-40be50b52382f40f87ea2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - SM(d16:1/18:2(9Z,11E)+=O(13)) 40V, Positive-QTOFsplash10-0udi-0000091100-33329e5425d8ce48ac232021-10-21Wishart 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 Compound156997901
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