Nicotinamide ribotide (YMDB00138)

Identification
YMDB IDYMDB00138
NameNicotinamide ribotide
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionNicotinamide ribotide, also known as NMN, belongs to the class of organic compounds known as nicotinamide nucleotides. These are pyridine nucleotides, in which the pyridine base is nicotinamide or a derivative thereof. Nicotinamide ribotide is an extremely weak basic (essentially neutral) compound (based on its pKa). Nicotinamide ribotide exists in all eukaryotes, ranging from yeast to humans. Within yeast, nicotinamide ribotide participates in a number of enzymatic reactions. In particular, nicotinamide ribotide can be biosynthesized from nicotinamide riboside through its interaction with the enzyme nicotinamide riboside kinase. In addition, nicotinamide ribotide can be converted into NAD through its interaction with the enzyme nicotinamide/nicotinic acid mononucleotide adenylyltransferase. In yeast, nicotinamide ribotide is involved in the metabolic pathway called the nad metabolism pathway.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • 3-(aminocarbonyl)-1-(5-O-phosphono-b-D-ribofuranosyl)-Pyridinium hydroxide inner salt
  • 3-(aminocarbonyl)-1-(5-O-phosphono-b-D-ribofuranosyl)-Pyridinium inner salt
  • 3-(aminocarbonyl)-1-(5-O-phosphono-beta-delta-ribofuranosyl)-Pyridinium hydroxide inner salt
  • 3-(aminocarbonyl)-1-(5-O-phosphono-beta-delta-ribofuranosyl)-Pyridinium inner salt
  • 3-Carbamoyl-1-b-D-ribofuranosylpyridinium hydroxide 5'-phosphate inner salt
  • 3-Carbamoyl-1-beta-delta-ribofuranosylpyridinium hydroxide 5'-phosphate inner salt
  • b-D-NMN
  • b-NMN
  • beta-delta-NMN
  • beta-Nicotinamide D-ribonucleotide
  • beta-Nicotinamide mononucleotide
  • beta-Nicotinamide ribonucleotide
  • beta-NMN
  • Nicotinamide D-ribonucleotide
  • Nicotinamide mononucleotide
  • Nicotinamide nucleotide
  • Nicotinamide ribonucleoside 5'-phosphate
  • Nicotinamide ribonucleotide
  • NMN
  • 3-(Aminocarbonyl)-1-(5-O-phosphonato-beta-D-ribofuranosyl)pyridinium
  • 3-(Aminocarbonyl)-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridinium, inner salt
  • 3-(Aminocarbonyl)-1-(5-O-phosphonato-b-D-ribofuranosyl)pyridinium
  • 3-(Aminocarbonyl)-1-(5-O-phosphonato-β-D-ribofuranosyl)pyridinium
  • 3-(Aminocarbonyl)-1-(5-O-phosphono-b-D-ribofuranosyl)pyridinium, inner salt
  • 3-(Aminocarbonyl)-1-(5-O-phosphono-β-D-ribofuranosyl)pyridinium, inner salt
  • b-Nicotinamide D-ribonucleotide
  • Β-nicotinamide D-ribonucleotide
  • b-Nicotinamide mononucleotide
  • Β-nicotinamide mononucleotide
  • b-Nicotinamide ribonucleotide
  • Β-nicotinamide ribonucleotide
  • Mononucleotide, nicotinamide
  • Bibenzoyl
  • Diphenylethanedione
  • Diphenylglyoxal
  • 1,2-Diphenylethane-1,2-dione
  • Diphenylethane-1,2-dione
  • Diphenyl-alpha-beta-ketone
  • Phosphatidylinositol 4,5-bisphosphoric acid
  • Diadenosine triphosphoric acid
  • Adenosine (5')triphospho(5')adenosine
  • Adenosine 5'-triphosphate 5'-adenosine
  • Adenosine(3)triphosphate adenosine
  • Adenosine(5')triphospho(5')adenosine
  • Bis(adenosine)-5'-triphosphate
  • p(1),p(3)-Bis(5'-adenosyl) trihydrogen triphosphate
  • p(1),p(3)-Bis(5'-adenosyl) triphosphate
  • p(1)-p(3)-Bis(5'-adenosyl) triphosphate
  • P1,P3-Bis(5'-adenosyl) triphosphate
  • Ap3a
  • 5'Ap3a
  • p(1),(P3)-Bis(5'-adenosyl)triphosphate
  • ApppA
  • Tetrahydrofolate
  • (6S)-Tetrahydrofolate
  • (6S)-Tetrahydrofolic acid
  • 5,6,7,8-Tetrahydrofolate
  • 5,6,7,8-Tetrahydrofolic acid
  • Tetra-H-folate
  • Tetrahydrafolate
  • Tetrahydropteroyl mono-L-glutamate
  • Tetrahydropteroylglutamate
  • 1,4-Butanediamine
  • 1,4-Butylenediamine
  • 1,4-DIAMINOBUTANE
  • 1,4-Tetramethylenediamine
  • Butane-1,4-diamine
  • Butylenediamine
  • H2N(CH2)4nh2
  • Putrescin
  • Putrescina
  • Putreszin
  • Tetramethylendiamin
  • Tetramethylenediamine
  • 1,4-Butanediammonium
  • Tetramethyldiamine
  • 1,4 Diaminobutane
  • 1,4 Butanediamine
CAS number1094-61-7
WeightAverage: 334.2192
Monoisotopic: 334.056601978
InChI KeyDAYLJWODMCOQEW-TURQNECASA-N
InChIInChI=1S/C11H15N2O8P/c12-10(16)6-2-1-3-13(4-6)11-9(15)8(14)7(21-11)5-20-22(17,18)19/h1-4,7-9,11,14-15H,5H2,(H3-,12,16,17,18,19)/t7-,8-,9-,11-/m1/s1
IUPAC Name3-carbamoyl-1-[(2R,3R,4S,5R)-5-[(hydrogen phosphonooxy)methyl]-3,4-dihydroxyoxolan-2-yl]-1lambda5-pyridin-1-ylium
Traditional IUPAC Name3-carbamoyl-1-[(2R,3R,4S,5R)-5-[(hydrogen phosphonooxy)methyl]-3,4-dihydroxyoxolan-2-yl]-1lambda5-pyridin-1-ylium
Chemical FormulaC11H15N2O8P
SMILES[H]O[C@]1([H])[C@]([H])(O[H])[C@]([H])(O[C@@]1([H])[N+]1=C([H])C(=C([H])C([H])=C1[H])C(=O)N([H])[H])C([H])([H])OP([O-])(=O)O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as nicotinamide nucleotides. These are pyridine nucleotides, in which the pyridine base is nicotinamide or a derivative thereof.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyridine nucleotides
Sub ClassNicotinamide nucleotides
Direct ParentNicotinamide nucleotides
Alternative Parents
Substituents
  • Nicotinamide-nucleotide
  • Pentose-5-phosphate
  • Pentose phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Monosaccharide phosphate
  • Nicotinamide
  • Pyridine carboxylic acid or derivatives
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyridinium
  • Pyridine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • 1,2-diol
  • Carboxamide group
  • Secondary alcohol
  • Primary carboxylic acid amide
  • Azacycle
  • Oxacycle
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organic zwitterion
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility4.16 g/LALOGPS
logP-1.5ALOGPS
logP-6.2ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.21ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area166.25 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity70.59 m³·mol⁻¹ChemAxon
Polarizability28.77 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • extracellular
  • mitochondrion
  • nucleus
  • peroxisome
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
NAD metabolismPW002421 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Nicotinate and nicotinamide metabolismec00760 Map00760
SMPDB Reactions
Nicotinamide ribotide + Adenosine triphosphate + hydron → Pyrophosphate + NAD
Nicotinamide riboside + Adenosine triphosphate → Nicotinamide ribotide + ADP + hydron
KEGG Reactions
NAD + water → Adenosine monophosphate + Nicotinamide ribotide + hydron
Adenosine triphosphate + hydron + Nicotinamide ribotide → Pyrophosphate + NAD
Adenosine triphosphate + hydron + Nicotinamide ribotide ↔ Pyrophosphate + NAD
Adenosine triphosphate + Nicotinamide riboside → hydron + Nicotinamide ribotide + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-006t-8902000000-75d46c23151f03298e05JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-01b9-4920300000-f0eec1327b9e3e217fddJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00di-1931000000-5aa0e5ba467b6bdbb57fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00dj-6920000000-4720b1b8ab108dc1b499JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-00mk-8903000000-042bd96d57e63adafe44JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-00di-3900000000-013c2f02e48342e61b5eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00di-3900000000-013c2f02e48342e61b5eJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1109000000-7e48df4297f6933ffc64JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002b-7419000000-c70e04daa2249a30318cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-9600000000-ec07884c9a438ebdba5aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-1009000000-623a45d318f08c622565JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-9002000000-a9b586e58b5858c6d213JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0032-9000000000-3fde5442f77c9f4b54b3JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • AbdelRaheim, S. R., Cartwright, J. L., Gasmi, L., McLennan, A. G. (2001). "The NADH diphosphatase encoded by the Saccharomyces cerevisiae NPY1 nudix hydrolase gene is located in peroxisomes." Arch Biochem Biophys 388:18-24.11361135
  • Natalini, P., Ruggieri, S., Raffaelli, N., Magni, G. (1986). "Nicotinamide mononucleotide adenylyltransferase. Molecular and enzymatic properties of the homogeneous enzyme from baker's yeast." Biochemistry 25:3725-3729.3013296
  • de Figueiredo, L. F., Gossmann, T. I., Ziegler, M., Schuster, S. (2011). "Pathway Analysis of NAD+ metabolism." Biochem J :.21729004
  • Anderson, R. M., Bitterman, K. J., Wood, J. G., Medvedik, O., Cohen, H., Lin, S. S., Manchester, J. K., Gordon, J. I., Sinclair, D. A. (2002). "Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels." J Biol Chem 277:18881-18890.11884393
  • Bieganowski, P., Brenner, C. (2004). "Discoveries of nicotinamide riboside as a nutrient and conserved NRK genes establish a Preiss-Handler independent route to NAD+ in fungi and humans." Cell 117:495-502.15137942
Synthesis Reference:Liu, Rihe; Visscher, Johannes. A novel preparation of nicotinamide mononucleotide. Nucleosides & Nucleotides (1994), 13(5), 1215-16.
External Links:
ResourceLink
CHEBI ID16171
HMDB IDHMDB00229
Pubchem Compound ID14180
Kegg IDC00455
ChemSpider ID13553
FOODB IDFDB021912
Wikipedia IDNot Available
BioCyc IDNICOTINAMIDE_NUCLEOTIDE

Enzymes

Protein Details
1. NADH pyrophosphatase
General function:
Involved in hydrolase activity
Specific function:
NAD(+) + H(2)O = AMP + NMN
Gene Name:
NPY1
Uniprot ID:
P53164
Molecular weight:
43516.0
Reactions
NAD(+) + H(2)O → AMP + NMN.
Protein Details
2. 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.
Protein Details
3. Nicotinamide-nucleotide adenylyltransferase 2
General function:
Involved in nucleotidyltransferase activity
Specific function:
ATP + nicotinamide ribonucleotide = diphosphate + NAD(+);ATP + nicotinate ribonucleotide = diphosphate + deamido-NAD+
Gene Name:
NMA2
Uniprot ID:
P53204
Molecular weight:
44908.69922
Reactions
ATP + nicotinamide ribonucleotide → diphosphate + NAD(+).
ATP + nicotinate ribonucleotide → diphosphate + deamido-NAD+
Protein Details
4. Nicotinamide-nucleotide adenylyltransferase 1
General function:
Involved in nucleotidyltransferase activity
Specific function:
ATP + nicotinamide ribonucleotide = diphosphate + NAD(+)
Gene Name:
NMA1
Uniprot ID:
Q06178
Molecular weight:
45858.60156
Reactions
ATP + nicotinamide ribonucleotide → diphosphate + NAD(+).