Hmdb loader
Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 03:37:00 UTC
Update Date2022-11-30 20:07:09 UTC
HMDB IDHMDB0290401
Secondary Accession NumbersNone
Metabolite Identification
Common NameSM(d17:2(4E,8Z)/20:3(8Z,11Z,14Z)-O(5,6))
DescriptionSM(d17:2(4E,8Z)/20:3(8Z,11Z,14Z)-O(5,6)) is a type of oxidized sphingolipid found in animal cell membranes. It usually consists of phosphorylcholine and ceramide. SM(d17:2(4E,8Z)/20:3(8Z,11Z,14Z)-O(5,6)) consists of a sphingosine backbone and a 5,6-epoxyeicosatrienoyl 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 FormulaC42H75N2O7P
Average Molecular Weight751.043
Monoisotopic Molecular Weight750.531189761
IUPAC Name(2-{[(2S,3R,4E,8Z)-3-hydroxy-2-(4-{3-[(2Z,5Z,8Z)-tetradeca-2,5,8-trien-1-yl]oxiran-2-yl}butanamido)heptadeca-4,8-dien-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E,8Z)-3-hydroxy-2-(4-{3-[(2Z,5Z,8Z)-tetradeca-2,5,8-trien-1-yl]oxiran-2-yl}butanamido)heptadeca-4,8-dien-1-yl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCC1OC1C\C=C/C\C=C/C\C=C/CCCCC)[C@H](O)\C=C\CC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C42H75N2O7P/c1-6-8-10-12-14-16-18-20-22-24-26-28-31-39(45)38(37-50-52(47,48)49-36-35-44(3,4)5)43-42(46)34-30-33-41-40(51-41)32-29-27-25-23-21-19-17-15-13-11-9-7-2/h15,17,20-23,27-29,31,38-41,45H,6-14,16,18-19,24-26,30,32-37H2,1-5H3,(H-,43,46,47,48)/b17-15-,22-20-,23-21-,29-27-,31-28+/t38-,39+,40?,41?/m0/s1
InChI KeyOFUXLZSXOUCGAL-NDXRODMJSA-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
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Oxacycle
  • Organoheterocyclic compound
  • Ether
  • Oxirane
  • Dialkyl ether
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organic zwitterion
  • Organooxygen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP4.84ALOGPS
logP5.56ChemAxon
logS-7.3ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area120.45 ŲChemAxon
Rotatable Bond Count34ChemAxon
Refractivity231.73 m³·mol⁻¹ChemAxon
Polarizability88.97 ųChemAxon
Number of Rings1ChemAxon
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]+281.72832859911
AllCCS[M+H-H2O]+281.51932859911
AllCCS[M+Na]+281.93332859911
AllCCS[M+NH4]+281.89132859911
AllCCS[M-H]-265.96532859911
AllCCS[M+Na-2H]-271.06932859911
AllCCS[M+HCOO]-276.68932859911
DeepCCS[M+H]+271.75930932474
DeepCCS[M-H]-269.37630932474
DeepCCS[M-2H]-302.59330932474
DeepCCS[M+Na]+277.530932474

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. 6.19 minutes32390414
Predicted by Siyang on May 30, 202229.2419 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.48 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4894.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid205.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid332.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid217.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid834.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1563.9 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 Acid843.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)501.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3398.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1037.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2970.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid918.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid719.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate242.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA181.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water11.3 seconds40023050

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
SM(d17:2(4E,8Z)/20:3(8Z,11Z,14Z)-O(5,6)),2TMS,isomer #1CCCCC/C=C\C/C=C\C/C=C\CC1OC1CCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CC/C=C\CCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C5013.5Semi standard non polar33892256
SM(d17:2(4E,8Z)/20:3(8Z,11Z,14Z)-O(5,6)),2TMS,isomer #1CCCCC/C=C\C/C=C\C/C=C\CC1OC1CCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CC/C=C\CCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C4760.8Standard non polar33892256
SM(d17:2(4E,8Z)/20:3(8Z,11Z,14Z)-O(5,6)),2TMS,isomer #1CCCCC/C=C\C/C=C\C/C=C\CC1OC1CCCC(=O)N([C@@H](COP(=O)([O-])OCC[N+](C)(C)C)[C@@H](/C=C/CC/C=C\CCCCCCCC)O[Si](C)(C)C)[Si](C)(C)C5428.4Standard polar33892256
Spectra
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 Compound156998147
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