sn-Glycero-3-phosphocholine (YMDB00694)

Identification
YMDB IDYMDB00694
Namesn-Glycero-3-phosphocholine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlycerophosphocholine belongs to the class of organic compounds known as glycerophosphocholines. These are lipids containing a glycerol moiety carrying a phosphocholine at the 3-position. Glycerophosphocholine is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • a-Glycerophosphorylcholine
  • a-Glycerylphosphorylcholine
  • alpha-Glycerophosphorylcholine
  • alpha-Glycerylphosphorylcholine
  • Choline Alfoscerate
  • Choline glycerophosphate
  • glycero-3-phosphocholine
  • Glycerol 3-phosphocholine
  • Glycerol phosphorylcholine
  • Glycerol-3-phosphatidylcholine
  • Glycerophosphatidylcholine
  • glycerophosphocholine
  • Glycerophosphorylcholine
  • GPC
  • GPCho
  • hydrogen glycerophosphate Choline
  • L-alpha-Glycerophosphocholine
  • L-alpha-Glycerophosphorylcholine
  • L-alpha-Glycerylphosphorylcholine
  • sn-glycero-3-phosphocholine
  • Glycerol 3 phosphocholine
  • 3-Phosphocholine, glycerol
  • Alphoscerate, choline
  • Alfoscerate, choline
  • Choline alphoscerate
  • Glycerophosphate, choline
  • Glycerylphosphorylcholine
  • L alpha Glycerylphosphorylcholine
CAS number563-24-6
WeightAverage: 258.2292
Monoisotopic: 258.110648921
InChI KeySUHOQUVVVLNYQR-MRVPVSSYSA-O
InChIInChI=1S/C8H20NO6P/c1-9(2,3)4-5-14-16(12,13)15-7-8(11)6-10/h8,10-11H,4-7H2,1-3H3/p+1/t8-/m1/s1
IUPAC Name[(2R)-2,3-dihydroxypropoxy][2-(trimethylazaniumyl)ethoxy]phosphinic acid
Traditional IUPAC Nameglycerylphosphorylcholine
Chemical FormulaC8H21NO6P
SMILESC[N+](C)(C)CCOP(O)(=O)OC[C@H](O)CO
Chemical Taxonomy
Description belongs to the class of organic compounds known as glycerophosphocholines. These are lipids containing a glycerol moiety carrying a phosphocholine at the 3-position.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphocholines
Direct ParentGlycerophosphocholines
Alternative Parents
Substituents
  • Glycero-3-phosphocholine
  • Phosphocholine
  • Dialkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • 1,2-diol
  • Secondary alcohol
  • Organic nitrogen compound
  • Alcohol
  • Organic salt
  • Hydrocarbon derivative
  • Primary alcohol
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Amine
  • Organic cation
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge1
Melting point142.5 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility4.04 g/LALOGPS
logP-2.5ALOGPS
logP-5.7ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area96.22 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity69.8 m³·mol⁻¹ChemAxon
Polarizability25.11 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cell Envelope, Cytoplasm, Endoplasmic Reticulum, Extracellular, Mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Choline metabolismPW002494 ThumbThumb?image type=greyscaleThumb?image type=simple
Ether lipid metabolismPW002492 ThumbThumb?image type=greyscaleThumb?image type=simple
Glycerophospholipid metabolismPW002493 ThumbThumb?image type=greyscaleThumb?image type=simple
Lysolipid incorporation into ERPW002532 ThumbThumb?image type=greyscaleThumb?image type=simple
Lysolipid incorporation into ER PC(10:0/10:0)PW002780 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Ether lipid metabolismec00565 Map00565
Glycerophospholipid metabolismec00564 Map00564
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-001j-6910000000-acf817052a0850477ae9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0019-9330000000-b51666237b4e073cf359JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-003i-9310000000-6c5dfdcbc5c98c1bb4caJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052r-9000000000-f898295a6e607b0f5d92JSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Lee, K. S., Patton, J. L., Fido, M., Hines, L. K., Kohlwein, S. D., Paltauf, F., Henry, S. A., Levin, D. E. (1994). "The Saccharomyces cerevisiae PLB1 gene encodes a protein required for lysophospholipase and phospholipase B activity." J Biol Chem 269:19725-19730.8051052
  • Murray, J. P., McMaster, C. R. (2005). "Nte1p-mediated deacylation of phosphatidylcholine functionally interacts with Sec14p." J Biol Chem 280:8544-8552.15611060
  • Merkel, O., Fido, M., Mayr, J. A., Pruger, H., Raab, F., Zandonella, G., Kohlwein, S. D., Paltauf, F. (1999). "Characterization and function in vivo of two novel phospholipases B/lysophospholipases from Saccharomyces cerevisiae." J Biol Chem 274:28121-28127.10497163
  • Fisher, E., Almaguer, C., Holic, R., Griac, P., Patton-Vogt, J. (2005). "Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae." J Biol Chem 280:36110-36117.16141200
  • Almaguer, C., Cheng, W., Nolder, C., Patton-Vogt, J. (2004). "Glycerophosphoinositol, a novel phosphate source whose transport is regulated by multiple factors in Saccharomyces cerevisiae." J Biol Chem 279:31937-31942.15145930
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID16870
HMDB IDHMDB00086
Pubchem Compound ID439285
Kegg IDC00670
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDAlpha-GPC
BioCyc IDGLYCERYLPHOSPHORYLCHOLINE

Enzymes

Protein Details
1. Glycerophosphodiester phosphodiesterase GDE1
General function:
Involved in protein binding
Specific function:
Glycerophosphocholine glycerophosphodiesterase responsible for the hydrolysis of intracellular glycerophosphocholine into glycerol-phosphate and choline. The choline is used for phosphatidyl-choline synthesis. Required for utilization of glycerophosphocholine as phosphate source
Gene Name:
GDE1
Uniprot ID:
Q02979
Molecular weight:
138013.0
Reactions
A glycerophosphodiester + H(2)O → an alcohol + sn-glycerol 3-phosphate.
Protein Details
2. Lysophospholipase 3
General function:
Involved in metabolic process
Specific function:
Sequentially removes both fatty acyl groups from diacylglycerophospholipids and therefore has both phospholipase A and lysophospholipase activities. Substrate preference is phosphatidylserine > phosphatidylinositol. Does not cleave phosphatidylcholine, phosphatidylethanolamine, phosphatidic acid and phosphatidylinositol-bisphosphate
Gene Name:
PLB3
Uniprot ID:
Q08108
Molecular weight:
75076.20313
Reactions
2-lysophosphatidylcholine + H(2)O → glycerophosphocholine + a carboxylate.
Protein Details
3. Lysophospholipase 1
General function:
Involved in metabolic process
Specific function:
Sequentially removes both fatty acyl groups from diacylglycerophospholipids and therefore has both phospholipase A and lysophospholipase activities. Substrate preference is phosphatidylserine > phosphatidylinositol >> phosphatidylcholine > phosphatidylethanolamine
Gene Name:
PLB1
Uniprot ID:
P39105
Molecular weight:
71666.60156
Reactions
2-lysophosphatidylcholine + H(2)O → glycerophosphocholine + a carboxylate.
Protein Details
4. Lysophospholipase NTE1
General function:
Involved in metabolic process
Specific function:
Intracellular phospholipase B that catalyzes the double deacylation of phosphatidylcholine (PC) to glycerophosphocholine (GroPCho). Plays an important role in membrane lipid homeostasis. Responsible for the rapid PC turnover in response to inositol, elevated temperatures, or when choline is present in the growth medium
Gene Name:
NTE1
Uniprot ID:
Q04958
Molecular weight:
187131.0
Reactions
2-lysophosphatidylcholine + H(2)O → glycerophosphocholine + a carboxylate.
Protein Details
5. Lysophospholipase 2
General function:
Involved in metabolic process
Specific function:
Sequentially removes both fatty acyl groups from diacylglycerophospholipids and therefore has both phospholipase A and lysophospholipase activities. Substrate preference is phosphatidylserine > phosphatidylinositol > phosphatidylcholine > phosphatidylethanolamine
Gene Name:
PLB2
Uniprot ID:
Q03674
Molecular weight:
75454.60156
Reactions
2-lysophosphatidylcholine + H(2)O → glycerophosphocholine + a carboxylate.

Transporters

Protein Details
1. Probable metabolite transport protein GIT1
General function:
Involved in transmembrane transporter activity
Specific function:
Not Available
Gene Name:
GIT1
Uniprot ID:
P25346
Molecular weight:
57321.19922