Showing metabocard for CDP-DG(16:0/18:1(11Z)) (BMDB0006970)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 23:27:52 UTC
Update Date2020-05-20 22:50:38 UTC
BMDB IDBMDB0006970
Secondary Accession Numbers
  • BMDB06970
Metabolite Identification
Common NameCDP-DG(16:0/18:1(11Z))
DescriptionCDP-DG(16:0/18:1(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(16:0/18:1(11Z)), 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(16:0/18:1(11Z)) is also a substrate of CDP-diacylglycerol pyrophosphatase. It is involved in CDP-diacylglycerol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
1-Hexadecanoyl-2-(11Z-octadecenoyl)-sn-glycero-3-CDPHMDB
1-Palmitoyl-2-vaccenoyl-sn-glycero-3-cytidine-5'-diphosphateHMDB
CDP-DG(16:0/18:1)HMDB
CDP-DG(16:0/18:1N7)HMDB
CDP-DG(16:0/18:1W7)HMDB
CDP-DG(34:1)HMDB
CDP-Diacylglycerol(16:0/18:1)HMDB
CDP-Diacylglycerol(16:0/18:1N7)HMDB
CDP-Diacylglycerol(16:0/18:1W7)HMDB
CDP-Diacylglycerol(34:1)HMDB
Chemical FormulaC46H83N3O15P2
Average Molecular Weight980.1098
Monoisotopic Molecular Weight979.529942025
IUPAC Name{[(2R,4S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-(hexadecanoyloxy)-2-[(11Z)-octadec-11-enoyloxy]propoxy](hydroxy)phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,4S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-(hexadecanoyloxy)-2-[(11Z)-octadec-11-enoyloxy]propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCCCCCCCCCCCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@@H](O)C1O)N1C=CC(N)=NC1=O)OC(=O)CCCCCCCCC\C=C/CCCCCC
InChI Identifier
InChI=1S/C46H83N3O15P2/c1-3-5-7-9-11-13-15-17-18-20-22-24-26-28-30-32-42(51)62-38(35-59-41(50)31-29-27-25-23-21-19-16-14-12-10-8-6-4-2)36-60-65(55,56)64-66(57,58)61-37-39-43(52)44(53)45(63-39)49-34-33-40(47)48-46(49)54/h13,15,33-34,38-39,43-45,52-53H,3-12,14,16-32,35-37H2,1-2H3,(H,55,56)(H,57,58)(H2,47,48,54)/b15-13-/t38-,39-,43?,44+,45-/m1/s1
InChI KeySUOOPPGQEZMSRO-PDKKHWMPSA-N
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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassCDP-glycerols
Direct ParentCDP-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 FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Intracellular membrane
  • Membrane
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP6.5ALOGPS
logP10.08ChemAxon
logS-5.4ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area263.27 ŲChemAxon
Rotatable Bond Count43ChemAxon
Refractivity250.53 m³·mol⁻¹ChemAxon
Polarizability108.33 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0920000101-ea6baebdf45bc88e5c89View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1920001000-759c7de95464117a82fcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3930000000-3254d7890aa7653df37eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0bt9-0690001103-4f74ac749916951ea91dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bti-5692200201-8d93f2d99c9b78989b01View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-5921000000-647a4569c3e602e928caView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-1000010039-085eaa0e1b2b6c93141bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-07w9-5000000095-e85380b06d89ab03cf6cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-0025910000-311121f7a00454550cadView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000001009-edcd69c729b370a00970View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004l-9071812302-4dbc8f5a66229b3c70faView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0c0r-6459401202-f58f95c67bcb4bf97908View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Intracellular membrane
  • Membrane
  • Mitochondria
Biospecimen Locations
  • All Tissues
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
All TissuesExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0006970
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB024164
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53477914
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
General function:
Lipid transport and metabolism
Specific function:
Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin.
Gene Name:
PGS1
Uniprot ID:
Q2KJ28
Molecular weight:
62732.0
Reactions
CDP-DG(16:0/18:1(11Z)) + Glycerol 3-phosphate → PGP(16:0/18:1(11Z)) + Cytidine monophosphatedetails
Enzyme Details
2. Phosphatidate cytidylyltransferase 2
General function:
Lipid transport and metabolism
Specific function:
Catalyzes the conversion of phosphatidic acid (PA) to CDP-diacylglycerol (CDP-DAG), an essential intermediate in the synthesis of phosphatidylglycerol, cardiolipin and phosphatidylinositol (By similarity). Exhibits specificity for the nature of the acyl chains at the sn-1 and sn-2 positions in the substrate, PA and the preferred acyl chain composition is 1-stearoyl-2-arachidonoyl-sn-phosphatidic acid (By similarity). Plays an important role in regulating the growth and maturation of lipid droplets which are storage organelles at the center of lipid and energy homeostasis (By similarity).
Gene Name:
CDS2
Uniprot ID:
A0JNC1
Molecular weight:
51357.0
Reactions
Cytidine triphosphate + PA(16:0/18:1(11Z)) → Pyrophosphate + CDP-DG(16:0/18:1(11Z))details