nicotinic acid D-ribonucleotide (YMDB00741)

Identification

YMDB ID

YMDB00741

Name

nicotinic acid D-ribonucleotide

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

nicotinate beta-D-ribonucleotide, also known as b-nicotinic acid D-ribonucleotide, belongs to the class of organic compounds known as purine ribonucleoside polyphosphates. These are purine ribobucleotides with polyphosphate (with 4 or more phosphate) group linked to the ribose moiety. nicotinate beta-D-ribonucleotide is an extremely weak basic (essentially neutral) compound (based on its pKa). In yeast, nicotinate beta-D-ribonucleotide is involved in the metabolic pathway called the nad metabolism pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

beta-nicotinate d-ribonucleotide
Nicotinate D-ribonucleotide
nicotinate ribonucleotide
nicotinic acid ribonucleotide
b-Nicotinate D-ribonucleotide
b-Nicotinic acid D-ribonucleotide
beta-Nicotinic acid D-ribonucleotide
β-Nicotinate D-ribonucleotide
β-Nicotinic acid D-ribonucleotide
Nicotinic acid D-ribonucleotide
Nicotinate b-D-ribonucleotide
Nicotinate β-D-ribonucleotide
Nicotinic acid b-D-ribonucleotide
Nicotinic acid beta-D-ribonucleotide
Nicotinic acid β-D-ribonucleotide
Nicotinate mononucleotide
Nicotinic acid mononucleotide
Deamido nicotinamide ribonucleotide
Deamido-NMN
Nicotinic acid ribotide
Nicotinic mononucleotide
beta-Nicotinic acid mononucleotide
β-Nicotinic acid mononucleotide

CAS number

Not Available

Weight

Average: 336.2119
Monoisotopic: 336.048442595

InChI Key

JOUIQRNQJGXQDC-ZYUZMQFOSA-O

InChI

InChI=1S/C11H14NO9P/c13-8-7(5-20-22(17,18)19)21-10(9(8)14)12-3-1-2-6(4-12)11(15)16/h1-4,7-10,13-14H,5H2,(H2-,15,16,17,18,19)/p+1/t7-,8-,9-,10-/m1/s1

IUPAC Name

3-carboxy-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1lambda5-pyridin-1-ylium

Traditional IUPAC Name

3-carboxy-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-1lambda5-pyridin-1-ylium

Chemical Formula

C₁₁H₁₅NO₉P

SMILES

O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)[N+]1=CC=CC(=C1)C(O)=O

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as nicotinic acid nucleotides. These are pyridine nucleotides, in which the pyridine base is nicotinic acid or a derivative thereof.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyridine nucleotides

Sub Class

Nicotinic acid nucleotides

Direct Parent

Nicotinic acid nucleotides

Alternative Parents

Substituents

Nicotinic-acid-nucleotide
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Pyridine carboxylic acid
Pyridine carboxylic acid or derivatives
Monoalkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyridine
Pyridinium
Alkyl phosphate
Vinylogous amide
Tetrahydrofuran
Heteroaromatic compound
Secondary alcohol
1,2-diol
Carboxylic acid derivative
Organoheterocyclic compound
Azacycle
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Organopnictogen compound
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Alcohol
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nicotinic acid mononucleotide (CHEBI:15763 )
Pyridine alkaloids (C01185 )

Physical Properties

State

Not Available

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	1.71 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-5.4	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	1.2	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	157.63 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	69.89 m³·mol⁻¹	ChemAxon
Polarizability	28.66 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Cytoplasm, Mitochondrion

Organoleptic Properties

Not Available

SMPDB Pathways

NAD metabolism

PW002421

KEGG Pathways

Nicotinate and nicotinamide metabolism

ec00760

SMPDB Reactions

Adenosine triphosphate + Nicotinate D-ribonucleoside → ADP + hydron + nicotinic acid D-ribonucleotide

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00kb-9704000000-b4f3d91df4a5fb88cc5e	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-000b-9221310000-f2425a1cc55147b91d2b	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-1009000000-227e6a4729b96a705fa4	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-002b-5239000000-223d08e3fd97af58d374	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9500000000-db23a80f58b7ac9781fd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-1009000000-f16974a59d3ff46358d6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-002b-9001000000-ca67d776dd7d3f5d4650	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-5808f9bb378f2d60cd9b	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0479000000-61da4c1926ec7950c051	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00si-5950000000-2c01c6fd1632660b38c7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-001i-9500000000-3dbb0f51364659db892e	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

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
Lu, S. P., Kato, M., Lin, S. J. (2009). "Assimilation of endogenous nicotinamide riboside is essential for calorie restriction-mediated life span extension in Saccharomyces cerevisiae." J Biol Chem 284:17110-17119.19416965
Magni, G., Amici, A., Emanuelli, M., Orsomando, G., Raffaelli, N., Ruggieri, S. (2004). "Structure and function of nicotinamide mononucleotide adenylyltransferase." Curr Med Chem 11:873-885.15078171

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	15763
HMDB ID	HMDB0001132
Pubchem Compound ID	121992
Kegg ID	C01185
ChemSpider ID	24785392
FOODB ID	FDB022444
Wikipedia ID	Not Available
BioCyc ID	NICOTINATE_NUCLEOTIDE

Enzymes

Protein Details

1. Nicotinate-nucleotide pyrophosphorylase [carboxylating]

General function:: Involved in catalytic activity
Specific function:: Involved in the catabolism of quinolinic acid (QA)
Gene Name:: BNA6
Uniprot ID:: P43619
Molecular weight:: 32364.69922

Reactions

Nicotinate D-ribonucleotide + diphosphate + CO(2) → pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate.

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(+).

Protein Details

5. Nicotinate phosphoribosyltransferase

General function:: Involved in nicotinate phosphoribosyltransferase activity
Specific function:: Essential for growth under anaerobic conditions
Gene Name:: NPT1
Uniprot ID:: P39683
Molecular weight:: 49018.19922

Reactions

Nicotinate D-ribonucleotide + diphosphate → nicotinate + 5-phospho-alpha-D-ribose 1-diphosphate.

nicotinic acid D-ribonucleotide (YMDB00741)

Structure for #<Compound:0xaca15a98>

Enzymes

Reactions

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