Record Information
Version2.0
Creation Date2012-08-09 09:25:05 -0600
Update Date2015-06-03 17:21:36 -0600
Secondary Accession Numbers
  • ECMDB21483
Identification
Name:2-5-Phosphoribosyl-3-dephospho-CoA
Description2-5-phosphoribosyl-3-dephospho-CoA is a member of the chemical class known as Purine 3'-deoxyribonucleoside Diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 3. This compound is an important cofactor for citrate lyase. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation.
Structure
Thumb
Synonyms:
  • 2'-(5''-Phosphoribosyl)-3'-dephospho-CoA
Chemical Formula:C26H43N7O19P3S
Weight:Average: 882.641
Monoisotopic: 882.154727455
InChI Key:KZAGRNGHZHVHLU-NNJMUBGFSA-K
InChI:InChI=1S/C26H46N7O19P3S/c1-26(2,20(37)23(38)29-4-3-16(34)28-5-6-56)10-48-55(44,45)52-54(42,43)47-8-13-7-14(24(49-13)33-12-32-17-21(27)30-11-31-22(17)33)50-25-19(36)18(35)15(51-25)9-46-53(39,40)41/h11-15,17-20,22,24-25,35-37,56H,3-10H2,1-2H3,(H,28,34)(H,29,38)(H,42,43)(H,44,45)(H2,27,30,31)(H2,39,40,41)/p-3/t13-,14+,15+,17?,18+,19+,20?,22?,24+,25+/m0/s1
CAS number:Not Available
IUPAC Name:4-({[({[(2S,4R,5R)-4-{[(2S,3R,4S,5R)-5-[(hydrogen phosphonatooxy)methyl]-3,4-dihydroxyoxolan-2-yl]oxy}-5-(6-imino-4,5,6,9-tetrahydro-3H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-3,3-dimethyl-N-{2-[(2-sulfanylethyl)carboximidato]ethyl}butanecarboximidate
Traditional IUPAC Name:4-[({[(2S,4R,5R)-4-{[(2S,3R,4S,5R)-5-[(hydrogen phosphonatooxy)methyl]-3,4-dihydroxyoxolan-2-yl]oxy}-5-(6-imino-4,5-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-2-hydroxy-3,3-dimethyl-N-{2-[(2-sulfanylethyl)carboximidato]ethyl}butanecarboximidate
SMILES:[H]C(O)(C([O-])=NCCC([O-])=NCCS)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@]1([H])C[C@@]([H])(O[C@]2([H])O[C@]([H])(COP(O)([O-])=O)[C@@]([H])(O)[C@@]2([H])O)[C@@]([H])(O1)N1C=NC2([H])C(=N)N=CNC12[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine 3'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 3.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 3'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 3'-deoxyribonucleoside diphosphate
  • Pentose-5-phosphate
  • Pentose phosphate
  • O-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Monosaccharide
  • 1,4,5,6-tetrahydropyrimidine
  • Hydropyrimidine
  • Tetrahydrofuran
  • 2-imidazoline
  • Secondary alcohol
  • Formamidine
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboximidamide
  • Carboximidic acid derivative
  • Carboximidic acid
  • Carboxylic acid amidine
  • Amidine
  • Alkylthiol
  • Acetal
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic anion
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.36 g/LALOGPS
logP-0.74ALOGPS
logP-3.7ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)1.13ChemAxon
pKa (Strongest Basic)5.01ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area394.94 ŲChemAxon
Rotatable Bond Count21ChemAxon
Refractivity217.69 m³·mol⁻¹ChemAxon
Polarizability77.09 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-6100000090-ae8cb2d1434e3688ca47View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00pi-9010000050-05956258a316b945baddView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-9100000000-c5314c0993e8166d97abView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-4100000090-2a782810fc553eeb10d8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003r-9200000010-92849241d154e531ac3fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-005a-9100000000-75d4d51e33d79df7f528View 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:
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25202407
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

General function:
Involved in [citrate (pro-3S)-lyase] ligase activity
Specific function:
Acetylation of prosthetic group (2-(5''-phosphoribosyl)- 3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase
Gene Name:
citC
Uniprot ID:
P77390
Molecular weight:
40077
Reactions
ATP + acetate + [citrate (pro-3S)-lyase](thiol form) = AMP + diphosphate + [citrate (pro-3S)-lyase](acetyl form).