You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

PGP(10:0/25:1(11Z)) (YMDB14178)

Identification
YMDB IDYMDB14178
NamePGP(10:0/25:1(11Z))
SpeciesSaccharomyces cerevisiae
StrainBrewer's yeast
DescriptionPGP(10:0/25:1(11Z)) belongs to the class of glycerophosphoglycerophosphates, also called phosphatidylglycerophosphates (PGPs). These lipids contain a common glycerophosphate skeleton linked to at least one fatty acyl chain and a glycero-3-phosphate moiety. As is the case with diacylglycerols, phosphatidylglycerophosphates can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. PGP(10:0/25:1(11Z)), in particular, consists of one decanoyl chain to the C-1 atom, and one 11Z-pentacosanoyl to the C-2 atom. In E. coli, PGPs can be found in the cytoplasmic membrane. The are synthesized by the addition of glycerol 3-phosphate to a CDP-diacylglycerol. In turn, PGPs are dephosphorylated to Phosphatidylglycerols (PGs) by the enzyme Phosphatidylglycerophosphatase.
Structure
Thumb
MOLSDFPDBSMILESInChI
SynonymsNot Available
CAS numberNot Available
WeightAverage: 843.026
Monoisotopic: 842.507416632
InChI KeyYEFVXMGMBYAQGA-UWJHZTDJSA-N
InChIInChI=1S/C41H80O13P2/c1-3-5-7-9-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-27-29-31-33-41(44)54-39(36-50-40(43)32-30-28-26-10-8-6-4-2)37-53-56(48,49)52-35-38(42)34-51-55(45,46)47/h19-20,38-39,42H,3-18,21-37H2,1-2H3,(H,48,49)(H2,45,46,47)/b20-19-/t38-,39+/m0/s1
IUPAC Name[(2S)-3-({[(2R)-3-(decanoyloxy)-2-[(11Z)-pentacos-11-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid
Traditional IUPAC Name(2S)-3-{[(2R)-3-(decanoyloxy)-2-[(11Z)-pentacos-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid
Chemical FormulaC41H80O13P2
SMILES[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC)OC(=O)CCCCCCCCC\C=C/CCCCCCCCCCCCC
Chemical Taxonomy
Description belongs to the class of organic compounds known as phosphatidylglycerophosphates. These are glycerophosphoglycerophosphates in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphoglycerophosphates
Direct ParentPhosphatidylglycerophosphates
Alternative Parents
Substituents
  • Diacylglycerophosphoglycerophosphate
  • Sn-glycerol-3-phosphate
  • Dialkyl phosphate
  • Monoalkyl phosphate
  • Fatty acid ester
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Dicarboxylic acid or derivatives
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00058 g/LALOGPS
logP7.34ALOGPS
logP11.79ChemAxon
logS-6.2ALOGPS
pKa (Strongest Acidic)1.35ChemAxon
pKa (Strongest Basic)-3.4ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area195.35 ŲChemAxon
Rotatable Bond Count44ChemAxon
Refractivity221.1 m³·mol⁻¹ChemAxon
Polarizability97.99 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Mitochondrion membrane
Organoleptic PropertiesNot Available
SMPDB Pathways
Cardiolipin Biosynthesis CL(10:0/25:1(11Z)/10:0/25:1(11Z))PW005866 ThumbThumb?image type=greyscaleThumb?image type=simple
Cardiolipin Biosynthesis CL(10:0/25:1(11Z)/10:0/25:1(9Z))PW005867 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
CDP-DG(10:0/25:1(11Z)) + Glycerol 3-phosphate → PGP(10:0/25:1(11Z)) + hydron + Cytidine monophosphate
PGP(10:0/25:1(11Z)) + water → phosphate + PG(10:0/25:1(11Z))
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-08i3-1927423280-0c5ba3defd6f0bd1fba0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0c29-3936214220-e56c32a7cb0558d2122bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9858030300-6396e28b0900514766fdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fi0-4913201030-678af1aab40d7e1a90c3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9410000000-0b1659e2ecf5df586a52JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-90448da6143d19a80e90JSpectraViewer
References
References:
  • Rattray JB, Schibeci A, Kidby DK. (1975). "Lipids of yeasts." Bacteriol Rev. 1975 Sep;39(3):197-231.240350
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Essential for the viability of mitochondrial petite mutant. Catalyzes the committed step to the synthesis of the acidic phospholipids
Gene Name:
PGS1
Uniprot ID:
P25578
Molecular weight:
59369.69922
Reactions
CDP-diacylglycerol + sn-glycerol 3-phosphate → CMP + 3(3-sn-phosphatidyl)-sn-glycerol 1-phosphate.
Protein Details
2. Phosphatidylglycerophosphatase GEP4, mitochondrial
General function:
Involved in phosphatidylglycerophosphatase activity
Specific function:
Phosphatidylglycerophosphatase involved in the biosynthesis of cardiolipin (CL), a unique dimeric phosphoglycerolipid predominantly present in mitochondrial membranes and which has important functions for cellular energy metabolism, mitochondrial dynamics and the initiation of apoptotic pathways. Required for the stability of respiratory chain supercomplexes and for growth at elevated temperature, in presence of ethidium bromide or in absence of prohibitins
Gene Name:
GEP4
Uniprot ID:
P38812
Molecular weight:
20944.90039
Reactions
Phosphatidylglycerophosphate + H(2)O → phosphatidylglycerol + phosphate.