CDP-DG(10:0/16:1(11Z)) (YMDB12076)

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Identification

YMDB ID

YMDB12076

Name

CDP-DG(10:0/16:1(11Z))

Species

Saccharomyces cerevisiae

Strain

Brewer's yeast

Description

CDP-DG(10:0/16:1(11Z)) belongs to the family of CDP-diacylglycerols. It is a glycerophospholipid containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part. As is the case with diacylglycerols, phosphatidylserines can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. CDP-DG(10:0/16:1(11Z)), in particular, consists of two decanoyl chain at positions C-1 and C2. In E. coli glycerophospholipid metabolism, The biosynthesis of CDP-diacylglycerol (CDP-DG) involves condensation of phosphatidic acid (PA) and cytidine triphosphate, with elimination of pyrophosphate, catalysed by the enzyme CDP-diacylglycerol synthase. The resulting CDP-diacylglycerol can be utilized immediately for the synthesis of phosphatidylglycerol (PG), and thence cardiolipin (CL), and of phosphatidylinositol (PI). CDP-DG(10:0/16:1(11Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

CAS number

Not Available

Weight

Average: 867.908
Monoisotopic: 867.404742465

InChI Key

RCOKTRLWMWZWKX-QLFIMROESA-N

InChI

InChI=1S/C38H67N3O15P2/c1-3-5-7-9-11-12-13-14-15-16-18-20-22-24-34(43)54-30(27-51-33(42)23-21-19-17-10-8-6-4-2)28-52-57(47,48)56-58(49,50)53-29-31-35(44)36(45)37(55-31)41-26-25-32(39)40-38(41)46/h9,11,25-26,30-31,35-37,44-45H,3-8,10,12-24,27-29H2,1-2H3,(H,47,48)(H,49,50)(H2,39,40,46)/b11-9-/t30-,31-,35+,36?,37-/m1/s1

IUPAC Name

{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-(decanoyloxy)-2-[(11Z)-hexadec-11-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid

Traditional IUPAC Name

[(2R,3R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-(decanoyloxy)-2-[(11Z)-hexadec-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

Chemical Formula

C₃₈H₆₇N₃O₁₅P₂

SMILES

[H][C@@](COC(=O)CCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCC\C=C/CCCC

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	0.039 g/L	ALOGPS
logP	4.44	ALOGPS
logP	6.53	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	1.86	ChemAxon
pKa (Strongest Basic)	-0.032	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	263.27 Å²	ChemAxon
Rotatable Bond Count	35	ChemAxon
Refractivity	213.72 m³·mol⁻¹	ChemAxon
Polarizability	91.56 Å³	ChemAxon
Number of Rings	2	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(10:0/16:1(11Z)/16:1(11Z)/20:1(13Z))	PW005332
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/16:1(11Z)/22:0)	PW005333
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/16:1(11Z)/22:1(11Z))	PW005334
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/16:1(11Z)/22:1(9Z))	PW005335
Cardiolipin Biosynthesis CL(10:0/16:1(11Z)/16:1(11Z)/24:0)	PW005336

KEGG Pathways

Not Available

SMPDB Reactions

PA(10:0/16:1(11Z)) + hydron + Cytidine triphosphate → Pyrophosphate + CDP-DG(10:0/16:1(11Z))

CDP-DG(10:0/16:1(11Z)) + Glycerol 3-phosphate → PGP(16:0/16:0) + hydron + Cytidine monophosphate

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	splash10-03di-0910001010-d7907e2fc55ec23a6991	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1910000000-fa15820b56d4d147a072	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-2920000000-c89a42c6eef026142897	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-11b9-0910001020-c3f607b4af1270003d9e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0h90-3901101000-ecbfcc46aa69ce38c8b9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bvi-4900000000-e102b03d8f389c0e6f04	JSpectraViewer
MS	Mass Spectrum (Electron Ionization)	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
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. Phosphatidate cytidylyltransferase

General function:: Involved in transferase activity, transferring phosphorus-containing groups
Specific function:: Supplies CDP-diacylglycerol, which may play an important role as both a precursor to phosphoinositide biosynthesis in the plasma membrane and as a negative effector of phosphatidylinositol 4-kinase activity, thereby exerting an effect on cell proliferation via a lipid-dependent signal transduction cascade
Gene Name:: CDS1
Uniprot ID:: P38221
Molecular weight:: 51822.39844

Reactions

CTP + phosphatidate → diphosphate + CDP-diacylglycerol.

Protein Details

3. Phosphatidate cytidylyltransferase, mitochondrial

General function:: CDP-diacylglycerol biosynthetic process
Specific function:: Catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid (PA) in the mitochondrial inner membrane. Required for the biosynthesis of the dimeric phospholipid cardiolipin, which stabilizes supercomplexes of the mitochondrial respiratory chain in the mitochondrial inner membrane.
Gene Name:: TAM41
Uniprot ID:: P53230
Molecular weight:: 44199.33

Reactions

Structure for #<Compound:0xa98d512c>

Enzymes

Reactions

Reactions

Reactions