CDP-DG(16:0/16:0) (YMDB12313)

Identification

YMDB ID

YMDB12313

Name

CDP-DG(16:0/16:0)

Species

Saccharomyces cerevisiae

Strain

Brewer's yeast

Description

CDP-DG(16:0/16:0) 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(16:0/16:0), in particular, consists of two hexadecanoyl 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(16:0/16:0) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

1,2-Dihexadecanoyl-rac-glycero-3-CDP
1,2-Dipalmitoyl-rac-glycero-3-cytidine-5'-diphosphate
CDP-DG(32:0)
CDP-Diacylglycerol(16:0/16:0)
CDP-Diacylglycerol(32:0)

CAS number

Not Available

Weight

Average: 954.086
Monoisotopic: 953.514292916

InChI Key

ITYHVANGBZMQML-QDFYKRCGSA-N

InChI

InChI=1S/C44H81N3O15P2/c1-3-5-7-9-11-13-15-17-19-21-23-25-27-29-39(48)57-33-36(60-40(49)30-28-26-24-22-20-18-16-14-12-10-8-6-4-2)34-58-63(53,54)62-64(55,56)59-35-37-41(50)42(51)43(61-37)47-32-31-38(45)46-44(47)52/h31-32,36-37,41-43,50-51H,3-30,33-35H2,1-2H3,(H,53,54)(H,55,56)(H2,45,46,52)/t36-,37-,41+,42?,43-/m1/s1

IUPAC Name

{[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-2,3-bis(hexadecanoyloxy)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)-2,3-bis(hexadecanoyloxy)propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

Chemical Formula

C₄₄H₈₁N₃O₁₅P₂

SMILES

[H][C@@](COC(=O)CCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H](C(O)[C@H]1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCCCCCCCC

Chemical Taxonomy

Description

belongs to the class of organic compounds known as cdp-diacylglycerols. These are glycerolipids containing a diacylglycerol, with a cytidine diphosphate attached to the oxygen O1 or O2 of the glycerol part.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

CDP-glycerols

Direct Parent

CDP-diacylglycerols

Alternative Parents

Substituents

Cdp-diacylglycerol
Pyrimidine ribonucleoside diphosphate
Diacyl-glycerol-3-pyrophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Pentose monosaccharide
Aminopyrimidine
Fatty acid ester
Pyrimidone
Monoalkyl phosphate
Imidolactam
Pyrimidine
Fatty acyl
Alkyl phosphate
Phosphoric acid ester
Dicarboxylic acid or derivatives
Hydropyrimidine
Organic phosphoric acid derivative
Monosaccharide
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
Amino acid or derivatives
1,2-diol
Carboxylic acid ester
Organoheterocyclic compound
Azacycle
Oxacycle
Carboxylic acid derivative
Alcohol
Organonitrogen compound
Organic nitrogen compound
Organooxygen compound
Amine
Carbonyl group
Primary amine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

CDP-diacylglycerols (LMGP13010003 )

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	0.0058 g/L	ALOGPS
logP	5.98	ALOGPS
logP	9.56	ChemAxon
logS	-5.2	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	42	ChemAxon
Refractivity	240.21 m³·mol⁻¹	ChemAxon
Polarizability	104.97 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	PW002431
Cardiolipin Biosynthesis CL(10:0/10:0/18:0/22:1(11Z))	PW003583
Cardiolipin Biosynthesis CL(10:0/10:0/18:1(11Z)/22:1(11Z))	PW003596
Cardiolipin Biosynthesis CL(10:0/10:0/18:1(9Z)/22:1(11Z))	PW003609
Cardiolipin Biosynthesis CL(10:0/10:0/20:0/22:1(11Z))	PW003624

KEGG Pathways

Not Available

SMPDB Reactions

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

DG(16:0/16:0/0:0) + hydron + Cytidine triphosphate → CDP-DG(16:0/16:0) + Pyrophosphate

PA(16:0/16:0) + hydron + Cytidine triphosphate Pyrophosphate + CDP-DG(16:0/16:0)

PA(10:0/22:1(11Z)) + hydron + Cytidine triphosphate → Pyrophosphate + CDP-DG(16:0/16:0)

PA(12:0/22:1(11Z)) + hydron + Cytidine triphosphate → Pyrophosphate + CDP-DG(16:0/16:0)

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	splash10-03di-0910001001-c3de6e15431b5ac5105e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1910001000-94fe74d873da591ba587	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3920010100-8cfc73d1ce30a6c32997	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4i-0980001205-1542b6ae52ff3efc590a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-5792301301-02cf7e042d4983495f65	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bt9-5910000000-476fcc03a8d550c335c6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2100010059-d69dd9d87d36fe9fe53c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btc-5000000192-0d1381c2685c4916fe9d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006w-0039300000-1610b6659c074d77d1cd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0000001009-3a3e7d7fc874243c5cc1	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0573-9050611301-a5605075e8ba8a1894b8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-053r-6439605102-0e715a1320fb44e4b4a2	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	HMDB0006968
Pubchem Compound ID	24779567
Kegg ID	Not Available
ChemSpider ID	24765809
FOODB ID	FDB024162
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. Cardiolipin synthase

General function:: Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:: Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
Gene Name:: CRD1
Uniprot ID:: Q07560
Molecular weight:: 32019.30078

Reactions

2 Phosphatidylglycerol → diphosphatidylglycerol + glycerol.

Protein Details

4. 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:0xa526a2a0>

Enzymes

Reactions

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Reactions

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