Hmdb loader
Survey
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2008-09-16 13:20:11 UTC
Update Date2022-07-14 16:57:35 UTC
HMDB IDHMDB0010397
Secondary Accession Numbers
  • HMDB10397
Metabolite Identification
Common NameLysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0)
DescriptionLysoPC(20:5(5Z,8Z,11Z,14Z,17Z)) is a lysophospholipid (LyP). It is a monoglycerophospholipid in which a phosphorylcholine moiety occupies a glycerol substitution site. Lysophosphatidylcholines can have different combinations of fatty acids of varying lengths and saturation attached at the C-1 (sn-1) position. Fatty acids containing 16, 18 and 20 carbons are the most common. LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)), in particular, consists of one chain of eicosapentaenoic acid at the C-1 position. The eicosapentaenoic acid moiety is derived from fish oils, liver and kidney. Lysophosphatidylcholine is found in small amounts in most tissues. It is formed by hydrolysis of phosphatidylcholine by the enzyme phospholipase A2, as part of the de-acylation/re-acylation cycle that controls its overall molecular species composition. It can also be formed inadvertently during extraction of lipids from tissues if the phospholipase is activated by careless handling. In blood plasma significant amounts of lysophosphatidylcholine are formed by a specific enzyme system, lecithin:cholesterol acyltransferase (LCAT), which is secreted from the liver. The enzyme catalyzes the transfer of the fatty acids of position sn-2 of phosphatidylcholine to the free cholesterol in plasma, with formation of cholesterol esters and lysophosphatidylcholine. Lysophospholipids have a role in lipid signaling by acting on lysophospholipid receptors (LPL-R). LPL-R's are members of the G protein-coupled receptor family of integral membrane proteins. LPL-R's are members of the G protein-coupled receptor (GPR) family of integral membrane proteins. Lysophosphatidylcholines (LPCs) specifically bind to GPR119, GPR40, GPR55 and GPR4.  binding of LPCs to GPR119, GPR40 and GPR55 induces intracellular calcium mobilization and leads to increased glucose-stimulated insulin secretion in different cell systems. In blood or plasma LPCs are bound mainly to albumin and to a lesser extent to lipoproteins. Inflammation, cell damage and other pathophysiological conditions can profoundly alter the ratio of free to albumin bound LPC through increased production of LPC or decreased plasma levels of albumin (PMID: 32599910 ). In particular, lower levels of albumin (hypoalbuminemia) lead to lower levels of LPC in the blood.  Hypoalbuminemia with albumin concentrations of <20 g/L are typical of patients with sepsis, burns or serious trauma (PMID: 26557421 ). Such low levels of albumin often lead to LPC levels that are 50-80 % lower than that seen in healthy individuals (PMID: 27501420 ). Decreased levels of LPC have been observed in a number of other inflammatory conditions beyond sepsis, including rheumatoid arthritis, diabetes, schizophrenia, polycystic ovary syndrome, Alzheimer’s disease, pulmonary arterial hypertension, aging, asthma and liver cirrhosis, where they were associated with increased mortality risk (PMID: 32599910 ).  LPCs have a number of protective or anti-inflammatory effects.  Higher levels of LPC induce cyclooxygenase-2 and endothelial nitric oxide synthase (eNOS) expression in endothelial cells, both of which can have vasoprotective effects either via production of prostacyclin or nitric oxide (PMID: 32599910 ). LPCs have been shown to elicit a number of effects on the innate immune system and effectively serve as dual-activity ligand molecules. In particular, LPCs directly activate toll-like receptor (TLR) 4 and TLR-2-1 receptors in the absence of classical TLR ligands. However, LPCs can also inhibit TLR-mediated signaling in the presence of classical TLR ligands, thereby acting as anti-inflammatory molecules (PMID: 32599910 ).  Low levels of LPC during a bacterial or viral infection with TLR-mediated signalling can lead to opposing (inflammatory vs. anti-inflammatory) effects and immune dysregulation.
Structure
Data?1582752823
Synonyms
ValueSource
1-Eicosapentaenoyl-glycero-3-phosphocholineHMDB
LPC(20:5)HMDB
LPC(20:5/0:0)HMDB
LPC(20:5n3/0:0)HMDB
LPC(20:5W3/0:0)HMDB
LyPC(20:5)HMDB
LyPC(20:5/0:0)HMDB
LyPC(20:5n3/0:0)HMDB
LyPC(20:5W3/0:0)HMDB
LysoPC(20:5)HMDB
LysoPC(20:5/0:0)HMDB
LysoPC(20:5n3/0:0)HMDB
LysoPC(20:5W3/0:0)HMDB
Lysophosphatidylcholine(20:5)HMDB
Lysophosphatidylcholine(20:5/0:0)HMDB
Lysophosphatidylcholine(20:5n3/0:0)HMDB
Lysophosphatidylcholine(20:5W3/0:0)HMDB
LysoPC(20:5(5Z,8Z,11Z,14Z,17Z))HMDB
1-(5Z,8Z,11Z,14Z,17Z-Eicosapentaenoyl)-glycero-3-phosphocholineHMDB
1-EicosapentaenoylglycerophosphocholineHMDB
Chemical FormulaC28H48NO7P
Average Molecular Weight541.657
Monoisotopic Molecular Weight541.316839407
IUPAC Name(2-{[(2R)-2-hydroxy-3-[(5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoyloxy]propyl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2R)-2-hydroxy-3-[(5Z,8Z,11Z,14Z,17Z)-icosa-5,8,11,14,17-pentaenoyloxy]propyl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@](O)([H])COP([O-])(=O)OCC[N+](C)(C)C
InChI Identifier
InChI=1S/C28H48NO7P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-28(31)34-25-27(30)26-36-37(32,33)35-24-23-29(2,3)4/h6-7,9-10,12-13,15-16,18-19,27,30H,5,8,11,14,17,20-26H2,1-4H3/b7-6-,10-9-,13-12-,16-15-,19-18-/t27-/m1/s1
InChI KeyPDIGSOAOQOXRDU-WJPZTBRDSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1-acyl-sn-glycero-3-phosphocholines. These are glycerophosphocholines in which the glycerol is esterified with a fatty acid at O-1 position, and linked at position 3 to a phosphocholine.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphocholines
Direct Parent1-acyl-sn-glycero-3-phosphocholines
Alternative Parents
Substituents
  • 1-acyl-sn-glycero-3-phosphocholine
  • Phosphocholine
  • Fatty acid ester
  • Dialkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Fatty acyl
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Organopnictogen compound
  • Carbonyl group
  • Organic salt
  • Amine
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Disposition
Process
Role
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 Solubility0.00035 g/LALOGPS
logP2.24ALOGPS
logP1.16ChemAxon
logS-6.2ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area105.12 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity166.26 m³·mol⁻¹ChemAxon
Polarizability59.35 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]+227.47130932474
DeepCCS[M-H]-225.57530932474
DeepCCS[M-2H]-258.81430932474
DeepCCS[M+Na]+233.29630932474
AllCCS[M+H]+236.732859911
AllCCS[M+H-H2O]+235.432859911
AllCCS[M+NH4]+238.032859911
AllCCS[M+Na]+238.332859911
AllCCS[M-H]-233.232859911
AllCCS[M+Na-2H]-236.832859911
AllCCS[M+HCOO]-240.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@](O)([H])COP([O-])(=O)OCC[N+](C)(C)C4523.8Standard polar33892256
LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@](O)([H])COP([O-])(=O)OCC[N+](C)(C)C3080.9Standard non polar33892256
LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCC(=O)OC[C@](O)([H])COP([O-])(=O)OCC[N+](C)(C)C3687.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0),1TMS,isomer #1CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)OC[C@H](COP(=O)([O-])OCC[N+](C)(C)C)O[Si](C)(C)C3704.5Semi standard non polar33892256
LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0),1TBDMS,isomer #1CC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CCCC(=O)OC[C@H](COP(=O)([O-])OCC[N+](C)(C)C)O[Si](C)(C)C(C)(C)C3937.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) GC-MS (1 TMS) - 70eV, Positivesplash10-00dv-9451030000-b3e7e6dc83cef8a1694f2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-13Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) GC-MS ("LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0),1TMS,#1" TMS) - 70eV, PositiveNot Available2021-10-14Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 10V, Positive-QTOFsplash10-006x-0000090000-966781e45a81e6ead19b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 20V, Positive-QTOFsplash10-001l-0900060000-b4ed895b41d16b1bef162021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 40V, Positive-QTOFsplash10-0ff0-0910040000-c4904cde31417b0828212021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 10V, Negative-QTOFsplash10-004i-0000090000-b3b193f52eedeabe6af52021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 20V, Negative-QTOFsplash10-0ufr-0009070000-2406648715055faa4dea2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 40V, Negative-QTOFsplash10-0udi-0039030000-604f34cf891a6521c09e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 10V, Positive-QTOFsplash10-03di-0000090000-1980164641e31388cc442021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 20V, Positive-QTOFsplash10-0bt9-0000090000-963e3d320bfe34c619682021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 40V, Positive-QTOFsplash10-0pc0-1609090000-325196b854dd9d78291d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 10V, Negative-QTOFsplash10-0006-0003090000-99431cfd188c484133742021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 20V, Negative-QTOFsplash10-0udi-1029010000-0382f363c2dbb3e1b30c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 40V, Negative-QTOFsplash10-0udi-1009000000-757c8d17c83dc69650c92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 10V, Positive-QTOFsplash10-0002-0000190000-271ce74a7fdc6d013cc32021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 20V, Positive-QTOFsplash10-000k-0002990000-1849ae288849291722e72021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - LysoPC(20:5(5Z,8Z,11Z,14Z,17Z)/0:0) 40V, Positive-QTOFsplash10-0pvr-0309400000-61ec2fdbb4c0e76306a12021-09-23Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
Tissue Locations
  • All Tissues
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1.608 +/- 0.163 uMAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB027548
KNApSAcK IDNot Available
Chemspider ID9931788
KEGG Compound IDC04230
BioCyc ID PHOSPHATIDYLCHOLINE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11757087
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 References
  1. Wernly B, Lichtenauer M, Hoppe UC, Jung C: Hyperglycemia in septic patients: an essential stress survival response in all, a robust marker for risk stratification in some, to be messed with in none. J Thorac Dis. 2016 Jul;8(7):E621-4. doi: 10.21037/jtd.2016.05.24. [PubMed:27501420 ]
  2. Knuplez E, Marsche G: An Updated Review of Pro- and Anti-Inflammatory Properties of Plasma Lysophosphatidylcholines in the Vascular System. Int J Mol Sci. 2020 Jun 24;21(12). pii: ijms21124501. doi: 10.3390/ijms21124501. [PubMed:32599910 ]
  3. Sun JK, Sun F, Wang X, Yuan ST, Zheng SY, Mu XW: Risk factors and prognosis of hypoalbuminemia in surgical septic patients. PeerJ. 2015 Oct 1;3:e1267. doi: 10.7717/peerj.1267. eCollection 2015. [PubMed:26557421 ]

Only showing the first 10 proteins. There are 29 proteins in total.

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes fatty acids from S-acylated cysteine residues in proteins such as trimeric G alpha proteins or HRAS. Has depalmitoylating activity and also low lysophospholipase activity.
Gene Name:
LYPLA1
Uniprot ID:
O75608
Molecular weight:
24669.355
General function:
Involved in phosphatidylcholine-sterol O-acyltransferase activity
Specific function:
Has transacylase and calcium-independent phospholipase A2 activity. Catalyzes the formation of 1-O-acyl-N-acetylsphingosine and the concomitant release of a lyso-phospholipid (By similarity). May have weak lysophospholipase activity.
Gene Name:
PLA2G15
Uniprot ID:
Q8NCC3
Molecular weight:
Not Available
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. This isozyme hydrolyzes more efficiently L-alpha-1-palmitoyl-2-oleoyl phosphatidylcholine than L-alpha-1-palmitoyl-2-arachidonyl phosphatidylcholine, L-alpha-1-palmitoyl-2-arachidonyl phosphatidylethanolamine, or L-alpha-1-stearoyl-2-arachidonyl phosphatidylinositol. May be involved in the production of lung surfactant, the remodeling or regulation of cardiac muscle.
Gene Name:
PLA2G5
Uniprot ID:
P39877
Molecular weight:
15674.065
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Hydrolyzes phosphatidylglycerol versus phosphatidylcholine with a 15-fold preference.
Gene Name:
PLA2G2F
Uniprot ID:
Q9BZM2
Molecular weight:
23256.29
General function:
Involved in metabolic process
Specific function:
Selectively hydrolyzes arachidonyl phospholipids in the sn-2 position releasing arachidonic acid. Together with its lysophospholipid activity, it is implicated in the initiation of the inflammatory response.
Gene Name:
PLA2G4A
Uniprot ID:
P47712
Molecular weight:
85210.19
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides.
Gene Name:
PLA2G1B
Uniprot ID:
P04054
Molecular weight:
16359.535
General function:
Involved in phospholipase A2 activity
Specific function:
Not known; does not seem to have catalytic activity.
Gene Name:
PLA2G12B
Uniprot ID:
Q9BX93
Molecular weight:
Not Available
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Has a powerful potency for releasing arachidonic acid from cell membrane phospholipids. Prefers phosphatidylethanolamine and phosphatidylcholine liposomes to those of phosphatidylserine.
Gene Name:
PLA2G10
Uniprot ID:
O15496
Molecular weight:
18153.04
General function:
Involved in phospholipase A2 activity
Specific function:
PA2 catalyzes the calcium-dependent hydrolysis of the 2-acyl groups in 3-sn-phosphoglycerides. Has a preference for arachidonic-containing phospholipids.
Gene Name:
PLA2G2E
Uniprot ID:
Q9NZK7
Molecular weight:
15988.525
General function:
Involved in hydrolase activity
Specific function:
May hydrolyze fatty acids from S-acylated cysteine residues in proteins such as trimeric G alpha proteins or HRAS. Has lysophospholipase activity (By similarity). Deacylates GAP43.
Gene Name:
LYPLA2
Uniprot ID:
O95372
Molecular weight:
24736.71

Only showing the first 10 proteins. There are 29 proteins in total.