PGP(16:1(11Z)/18:0) (YMDB14405)

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

Identification

YMDB ID

YMDB14405

Name

PGP(16:1(11Z)/18:0)

Species

Saccharomyces cerevisiae

Strain

Brewer's yeast

Description

PGP(16:1(11Z)/18:0) 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)/18:0), in particular, consists of one 11Z-hexadecenoyl chain to the C-1 atom, and one octadecanoyl 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: 828.999
Monoisotopic: 828.491766568

InChI Key

WQPWMUCEIPPMEU-DETHTZBZSA-N

InChI

InChI=1S/C40H78O13P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-40(43)53-38(36-52-55(47,48)51-34-37(41)33-50-54(44,45)46)35-49-39(42)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2/h10,12,37-38,41H,3-9,11,13-36H2,1-2H3,(H,47,48)(H2,44,45,46)/b12-10-/t37-,38+/m0/s1

IUPAC Name

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

Traditional IUPAC Name

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

Chemical Formula

C₄₀H₇₈O₁₃P₂

SMILES

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

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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoglycerophosphates

Direct Parent

Phosphatidylglycerophosphates

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 Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	0.00071 g/L	ALOGPS
logP	7.11	ALOGPS
logP	11.34	ChemAxon
logS	-6.1	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	43	ChemAxon
Refractivity	216.5 m³·mol⁻¹	ChemAxon
Polarizability	95.86 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)/18:0/16:1(11Z)/18:0)	PW012730
Cardiolipin Biosynthesis CL(16:1(11Z)/18:0/16:1(9Z)/18:0)	PW012731
Cardiolipin Biosynthesis CL(16:1(11Z)/18:0/18:0/18:0)	PW012732
Cardiolipin Biosynthesis CL(16:1(11Z)/18:0/18:0/18:1(11Z))	PW012733
Cardiolipin Biosynthesis CL(16:1(11Z)/18:0/18:0/18:1(9Z))	PW012734

KEGG Pathways

Not Available

SMPDB Reactions

CDP-DG(16:1(11Z)/18:0) + Glycerol 3-phosphate → PGP(16:1(11Z)/18:0) + hydron + Cytidine monophosphate

PGP(16:1(11Z)/18:0) + water → phosphate + PG(16:1(11Z)/18:0)

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	splash10-02dr-0290050150-7e8350f7a9f25365ca16	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0cg1-2391021110-926cfcc90ac0fc6d3f15	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-6393120100-409f632bb80341382786	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0fc9-3090020020-9fc99cbd00d7cb8077e0	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fb9-9060000000-3d950ec17d0dfd69d94b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9010000000-ae85728afde1e9a1864e	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	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:0x94409f54>

Enzymes

Reactions

Reactions