Dephospho-CoA (YMDB00357)

Identification
YMDB IDYMDB00357
NameDephospho-CoA
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDephospho-CoA, also known as 3'-dephospho-CoA, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Thus, dephospho-CoA is considered to be a fatty ester lipid molecule. Dephospho-CoA is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Dephospho-CoA exists in all living species, ranging from bacteria to humans. Within yeast, dephospho-CoA participates in a number of enzymatic reactions. In particular, dephospho-CoA can be biosynthesized from 4'-phosphopantetheine; which is mediated by the enzyme phosphopantetheine adenylyltransferase. In addition, dephospho-CoA can be converted into coenzyme A; which is mediated by the enzyme dephospho-CoA kinase. In yeast, dephospho-CoA is involved in the metabolic pathway called pantothenate and coa biosynthesis pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 3'-dephospho-CoA
  • 3'-dephospho-Coenzyme A
  • 3'-O-dephosphono-CoA
  • 3'-O-dephosphono-Coenzyme A
  • Dephospho-CoA
  • Dephospho-Coenzyme A
  • dephosphocoenzyme a
  • DpCoA
  • Dephospho CoA
  • 3'-Desphospho-coenzyme A
  • 2'-(5''-Triphosphoribosyl)-3'-dephospho-CoA
  • Desphospho-CoA
CAS number3633-59-8
WeightAverage: 687.554
Monoisotopic: 687.148877955
InChI KeyKDTSHFARGAKYJN-DRCCLKDXSA-N
InChIInChI=1S/C21H35N7O13P2S/c1-21(2,16(32)19(33)24-4-3-12(29)23-5-6-44)8-39-43(36,37)41-42(34,35)38-7-11-14(30)15(31)20(40-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-32,44H,3-8H2,1-2H3,(H,23,29)(H,24,33)(H,34,35)(H,36,37)(H2,22,25,26)/t11-,14-,15-,16?,20-/m1/s1
IUPAC Name[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][3-hydroxy-2,2-dimethyl-3-({2-[(2-sulfanylethyl)carbamoyl]ethyl}carbamoyl)propoxy]phosphinic acid
Traditional IUPAC Name{[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(3-hydroxy-2,2-dimethyl-3-({2-[(2-sulfanylethyl)carbamoyl]ethyl}carbamoyl)propoxy)phosphinic acid
Chemical FormulaC21H35N7O13P2S
SMILES[H]OC([H])(C(=O)N([H])C([H])([H])C([H])([H])C(=O)N([H])C([H])([H])C([H])([H])S[H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])[C@@]1([H])O[C@@]([H])(N2C([H])=NC3=C2N=C([H])N=C3N([H])[H])[C@]([H])(O[H])[C@]1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Pentose monosaccharide
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • N-acyl-amine
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Fatty amide
  • Imidolactam
  • Monosaccharide
  • Fatty acyl
  • Phosphoric acid ester
  • Alkyl phosphate
  • Azole
  • Heteroaromatic compound
  • Imidazole
  • Tetrahydrofuran
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Amino acid or derivatives
  • Carboxamide group
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Alkylthiol
  • Oxacycle
  • Azacycle
  • Organic oxide
  • Organooxygen compound
  • Organosulfur compound
  • Carbonyl group
  • Organopnictogen compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Alcohol
  • Organonitrogen compound
  • Primary amine
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility2.56 g/LALOGPS
logP-0.98ALOGPS
logP-5.9ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)5ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area300.03 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity151.87 m³·mol⁻¹ChemAxon
Polarizability62.51 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
  • lipid particle
  • endoplasmic reticulum
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pantothenate and CoA biosynthesisPW002463 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW002381 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pantothenate and CoA biosynthesisec00770 Map00770
beta-Alanine metabolismec00410 Map00410
SMPDB Reactions
4'-phosphopantetheine + Adenosine triphosphate + hydron → Pyrophosphate + Dephospho-CoA
Dephospho-CoA + Adenosine triphosphate → hydron + ADP + Coenzyme A
4'-phosphopantetheine + Adenosine triphosphate + hydron → Pyrophosphate + Dephospho-CoA
Adenosine triphosphate + hydron + Dephospho-CoA → Adenine + 2'-(5-Triphosphoribosyl)-3'-dephospho-CoA
KEGG Reactions
Adenosine triphosphate + Dephospho-CoA → hydron + Coenzyme A + ADP
Adenosine triphosphate + Pantetheine 4'-phosphate + hydron → Pyrophosphate + Dephospho-CoA
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03fr-1452933000-479a35a051c9c3fcda0dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-2930102000-19d2796dee5d14788e39JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-3930000000-d4541feacee9a6c7a4e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-4900000000-1307cbce80b215d981b9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0040-2910618000-58e100b1447a771ecd7cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1910200000-ba57f132dee9798389faJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-3900000000-d382c7ac6874be7ea151JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15468
HMDB IDHMDB01373
Pubchem Compound ID444485
Kegg IDC00882
ChemSpider ID388463
FOODB IDFDB022585
Wikipedia IDNot Available
BioCyc IDDEPHOSPHO-COA

Enzymes

Protein Details
1. Dephospho-CoA kinase CAB5
General function:
Involved in dephospho-CoA kinase activity
Specific function:
Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A
Gene Name:
CAB5
Uniprot ID:
Q03941
Molecular weight:
27339.5
Reactions
ATP + 3'-dephospho-CoA → ADP + CoA.
Protein Details
2. Uncharacterized protein YGR277C
General function:
Involved in nucleotidyltransferase activity
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
P53332
Molecular weight:
34306.30078
Reactions
ATP + pantetheine 4'-phosphate → diphosphate + 3'-dephospho-CoA.