You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Nicotinate D-ribonucleoside (YMDB00157)

Identification
YMDB IDYMDB00157
NameNicotinate D-ribonucleoside
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionNicotinate D-ribonucleoside, also known as nicotinic acid riboside or beta-D-ribosylnicotinate, belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). Nicotinate D-ribonucleoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Nicotinate D-ribonucleoside exists in all living species, ranging from bacteria to humans. nicotinate D-ribonucleoside can be converted into nicotinate β-D-ribonucleotide; which is catalyzed by the enzyme nicotinamide riboside kinase. In yeast, nicotinate D-ribonucleoside is involved in the metabolic pathway called the nad metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • D-ribosylnicotinate
  • Nicotinate riboside
  • nicotinic acid ribose
  • nicotinic acid riboside
  • ribosylnicotinate
  • beta-D-Ribosylnicotinate
  • b-D-Ribosylnicotinate
  • b-D-Ribosylnicotinic acid
  • beta-D-Ribosylnicotinic acid
  • Β-D-ribosylnicotinate
  • Β-D-ribosylnicotinic acid
  • Nicotinic acid D-ribonucleoside
  • Nicotinate ribonucleoside
  • Nicotinate ribose
  • Nicotinic acid ribonucleoside
  • 3-Carboxy-1-beta-D-ribofuranosylpyridinium
  • 3-Carboxy-1-β-D-ribofuranosylpyridinium
  • Nicotinic riboside
CAS numberNot Available
WeightAverage: 256.232
Monoisotopic: 256.082112185
InChI KeyPUEDDPCUCPRQNY-ZYUZMQFOSA-O
InChIInChI=1S/C11H13NO6/c13-5-7-8(14)9(15)10(18-7)12-3-1-2-6(4-12)11(16)17/h1-4,7-10,13-15H,5H2/p+1/t7-,8-,9-,10-/m1/s1
IUPAC Name3-carboxy-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium
Traditional IUPAC Name3-carboxy-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1lambda5-pyridin-1-ylium
Chemical FormulaC11H14NO6
SMILES[H]OC(=O)C1=C([H])C([H])=C([H])[N+](=C1[H])[C@]1([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyridine carboxylic acid
  • Pyridine carboxylic acid or derivatives
  • Monosaccharide
  • Pyridine
  • Pyridinium
  • Vinylogous amide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Oxacycle
  • Azacycle
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organonitrogen compound
  • Alcohol
  • Primary alcohol
  • Organic nitrogen compound
  • Organic cation
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge1
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility5.34 g/LALOGPS
logP-1.9ALOGPS
logP-5.3ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)2.76ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area111.1 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity59.01 m³·mol⁻¹ChemAxon
Polarizability24.21 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
NAD metabolismPW002421 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Nicotinate and nicotinamide metabolismec00760 Map00760
SMPDB Reactions
Adenosine triphosphate + Nicotinate D-ribonucleoside → ADP + hydron + nicotinic acid D-ribonucleotide
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-009f-9640000000-9ecd90015c00728b3b07JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-0fa9-9442740000-0573803f81575b22f5c8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0190000000-c2d0a64c0eb3d4ae2bfaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-0490000000-bb44dd196c6e9a647df7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0zgu-9600000000-d17b549da8f5e8b2dd2bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0090000000-384ec325284b36db888bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002b-2190000000-5ab972cf9d81893b8388JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9510000000-8e2f234fa7933273a714JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-06e9-1950000000-ae12a3b253bcd6d48cccJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9510000000-cb2cf76989881501793cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-9100000000-9d7edc1ec5f0c17e5711JSpectraViewer
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
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • de Figueiredo, L. F., Gossmann, T. I., Ziegler, M., Schuster, S. (2011). "Pathway Analysis of NAD+ metabolism." Biochem J :.21729004
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID27748
HMDB IDHMDB06809
Pubchem Compound ID161234
Kegg IDC05841
ChemSpider ID141636
FOODB IDFDB024094
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Nicotinamide riboside kinase
General function:
Involved in ATP binding
Specific function:
Catalyzes the phosphorylation of nicotinamide riboside (NR) and nicotinic acid riboside (NaR) to form nicotinamide mononucleotide (NMN) and nicotinic acid mononucleotide (NaMN)
Gene Name:
NRK1
Uniprot ID:
P53915
Molecular weight:
27689.30078
Reactions
ATP + N-ribosylnicotinamide → ADP + nicotinamide ribonucleotide.
ATP + D-ribosylnicotinate → ADP + nicotinate D-ribonucleotide.