Dephospho-CoA (ECMDB01373) (M2MDB000362)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (926)
Record Information
Version2.0
Creation Date2012-05-31 13:51:14 -0600
Update Date2015-09-13 12:56:11 -0600
Secondary Accession Numbers
  • ECMDB01373
Identification
Name:Dephospho-CoA
DescriptionDephospho-CoA is a substrate for Ectonucleotide pyrophosphatase/phosphodiesterase 1, Ectonucleotide pyrophosphatase/phosphodiesterase 3 and Ectonucleotide pyrophosphatase/phosphodiesterase 2.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 3'-dephospho-CoA
  • 3'-dephospho-Coenzyme A
  • 3'-O-Dephosphono-CoA
  • 3'-O-Dephosphono-Coenzyme A
  • 3-Dephospho-CoA
  • DePCoA
  • Dephospho-CoA
  • Dephospho-Coenzyme A
  • Dephosphocoenzyme a
Chemical Formula:C21H35N7O13P2S
Weight:Average: 687.554
Monoisotopic: 687.148877955
InChI Key:KDTSHFARGAKYJN-DRCCLKDXSA-N
InChI:InChI=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
CAS number:3633-59-8
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
SMILES:CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=CN=C2N)C(O)C(=O)NCCC(=O)NCCS
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
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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:Cytoplasm
Reactions:
Adenosine triphosphate + Dephospho-CoA <> ADP + Coenzyme A + Hydrogen ion
Adenosine triphosphate + Dephospho-CoA > 2'-(5-Triphosphoribosyl)-3'-dephospho-CoA + Adenine
Adenosine triphosphate + Hydrogen ion + Pantetheine 4'-phosphate <> Dephospho-CoA + Pyrophosphate
Adenosine triphosphate + Dephospho-CoA <> ADP + Coenzyme A
Adenosine triphosphate + Pantetheine 4'-phosphate <> Pyrophosphate + Dephospho-CoA
Hydrogen ion + Dephospho-CoA + Adenosine triphosphate > 2'-(5-Triphosphoribosyl)-3'-dephospho-CoA + Adenine
Dephospho-CoA + Adenosine triphosphate > Hydrogen ion + Coenzyme A + ADP
Adenosine triphosphate + Dephospho-CoA <> 2'-(5-Triphosphoribosyl)-3'-dephospho-CoA + Adenine
Pantetheine 4'-phosphate + Adenosine triphosphate + pantotheine 4'-phosphate > Dephospho-CoA + Pyrophosphate
Adenosine triphosphate + Dephospho-CoA > Adenosine diphosphate + Coenzyme A + ADP
Dephospho-CoA + Water <> Pantetheine 4'-phosphate + Adenosine monophosphate + pantotheine 4'-phosphate
4'-phosphopantetheine + Adenosine triphosphate + Hydrogen ion + 4'-phosphopantetheine > Pyrophosphate + Dephospho-CoA
Dephospho-CoA + Adenosine triphosphate > Hydrogen ion + Adenosine diphosphate + Coenzyme A + ADP
Adenosine triphosphate + Hydrogen ion + Pantetheine 4'-phosphate <> Dephospho-CoA + Pyrophosphate
Adenosine triphosphate + Dephospho-CoA <> ADP + Coenzyme A + Hydrogen ion
Adenosine triphosphate + Hydrogen ion + Pantetheine 4'-phosphate <> Dephospho-CoA + Pyrophosphate
SMPDB Pathways:
Citrate lyase activationPW002075 ThumbThumb?image type=greyscaleThumb?image type=simple
Pantothenate and CoA biosynthesisPW000828 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • 2'-(5'-phosphoribosyl)-3'-dephospho-CoA biosynthesis I (citrate lyase) P2-PWY
  • coenzyme A biosynthesis COA-PWY
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03fr-1452933000-479a35a051c9c3fcda0dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-2930102000-19d2796dee5d14788e39View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-3930000000-d4541feacee9a6c7a4e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000i-4900000000-1307cbce80b215d981b9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0040-2910618000-58e100b1447a771ecd7cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-1910200000-ba57f132dee9798389faView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a7i-3900000000-d382c7ac6874be7ea151View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Haugen HF, Skrede S: Nucleotide pyrophosphatase and phosphodiesterase I. Demonstration of activity in normal serum, and an increase in cholestatic liver disease. Scand J Gastroenterol. 1976;11(2):121-7. Pubmed: 4880
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID15468
HMDB IDHMDB01373
Pubchem Compound ID444485
Kegg IDC00882
ChemSpider ID388463
Wikipedia IDNot Available
BioCyc IDDEPHOSPHO-COA
EcoCyc IDDEPHOSPHO-COA

Enzymes

Protein Details
1. Phosphopantetheine adenylyltransferase
General function:
Involved in catalytic activity
Specific function:
Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
Gene Name:
coaD
Uniprot ID:
P0A6I6
Molecular weight:
17837
Reactions
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA.
Protein Details
2. Dephospho-CoA kinase
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:
coaE
Uniprot ID:
P0A6I9
Molecular weight:
22622
Reactions
ATP + 3'-dephospho-CoA = ADP + CoA.
Protein Details
3. 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A synthase
General function:
Involved in ATP binding
Specific function:
Catalyzes the formation of 2-(5''-triphosphoribosyl)-3'- dephosphocoenzyme-A, the precursor of the prosthetic group of the holo-acyl carrier protein (gamma chain) of citrate lyase, from ATP and dephospho-CoA
Gene Name:
citG
Uniprot ID:
P77231
Molecular weight:
31644
Reactions
ATP + 3-dephospho-CoA = 2'-(5-triphosphoribosyl)-3'-dephospho-CoA + adenine.