PGP(16:1(11Z)/20:0) (YMDB14408)

Identification

YMDB ID

YMDB14408

Name

PGP(16:1(11Z)/20:0)

Species

Saccharomyces cerevisiae

Strain

Brewer's yeast

Description

PGP(16:1(11Z)/20:0) 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(16:1(11Z)/20:0), in particular, consists of one 11Z-hexadecenoyl chain to the C-1 atom, and one eicosanoyl 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

MOL SDF PDB SMILES InChI

Synonyms

Not Available

CAS number

Not Available

Weight

Average: 857.053
Monoisotopic: 856.523066696

InChI Key

IZAYIYRXFKPMJE-IQTDMNHTSA-N

InChI

InChI=1S/C42H82O13P2/c1-3-5-7-9-11-13-15-17-18-19-20-22-24-26-28-30-32-34-42(45)55-40(38-54-57(49,50)53-36-39(43)35-52-56(46,47)48)37-51-41(44)33-31-29-27-25-23-21-16-14-12-10-8-6-4-2/h10,12,39-40,43H,3-9,11,13-38H2,1-2H3,(H,49,50)(H2,46,47,48)/b12-10-/t39-,40+/m0/s1

IUPAC Name

[(2S)-3-({[(2R)-3-[(11Z)-hexadec-11-enoyloxy]-2-(icosanoyloxy)propoxy](hydroxy)phosphoryl}oxy)-2-hydroxypropoxy]phosphonic acid

Traditional IUPAC Name

(2S)-3-{[(2R)-3-[(11Z)-hexadec-11-enoyloxy]-2-(icosanoyloxy)propoxy(hydroxy)phosphoryl]oxy}-2-hydroxypropoxyphosphonic acid

Chemical Formula

C₄₂H₈₂O₁₃P₂

SMILES

[H][C@](O)(COP(O)(O)=O)COP(O)(=O)OC[C@@]([H])(COC(=O)CCCCCCCCC\C=C/CCCC)OC(=O)CCCCCCCCCCCCCCCCCCC

Chemical Taxonomy

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	0.00055 g/L	ALOGPS
logP	7.5	ALOGPS
logP	12.23	ChemAxon
logS	-6.2	ALOGPS
pKa (Strongest Acidic)	1.35	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	195.35 Å²	ChemAxon
Rotatable Bond Count	45	ChemAxon
Refractivity	225.7 m³·mol⁻¹	ChemAxon
Polarizability	100.14 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Mitochondrion membrane

Organoleptic Properties

Not Available

SMPDB Pathways

Cardiolipin Biosynthesis CL(16:1(11Z)/20:0/16:1(11Z)/20:0)	PW012776
Cardiolipin Biosynthesis CL(16:1(11Z)/20:0/16:1(9Z)/20:0)	PW012777

KEGG Pathways

Not Available

SMPDB Reactions

CDP-DG(16:1(11Z)/20:0) + Glycerol 3-phosphate → PGP(16:1(11Z)/20:0) + hydron + Cytidine monophosphate

PGP(16:1(11Z)/20:0) + water → phosphate + PG(16:1(11Z)/20:0)

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4s-1291023250-02707e4e2d2a46de5cd2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-052k-2391012110-a9f3c4153f52f33eb188	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4j-7493111300-992b1c230e176c44a9e2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-1173-3091021020-cb581e417c85040b31c5	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fb9-9050000000-76afd93dc3c142f3a3d2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-6ee46fc53b0cada409da	JSpectraViewer

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:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	Not Available
Kegg ID	Not Available
ChemSpider ID	Not Available
FOODB ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not 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.

Structure for #<Compound:0xaf517480>

Enzymes

Reactions

Reactions