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Glycineamideribotide (YMDB00374)

Identification
YMDB IDYMDB00374
NameGlycineamideribotide
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGlycineamideribotide, also known as GAR, belongs to the class of organic compounds known as glycinamide ribonucleotides. Glycinamide ribonucleotides are compounds in which the amide N atom of glycineamide is linked to the C-1 of a ribosyl (or deoxyribosyl) moiety. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety. Glycineamideribotide exists in all living species, ranging from bacteria to plants to humans. In yeast, glycineamideribotide is involved in the metabolic pathway called the one carbon pool by folate I pathway. Based on a literature review very few articles have been published on Glycineamideribotide.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 5'-Phosphoribosyl-glycineamide
  • 5'-Phosphoribosylglycinamide
  • 5'-Phosphoribosylglycineamide
  • GAR
  • Glycinamide ribonucleotide
  • Glycineamide ribonucleotide
  • N-glycyl-5-O-phosphono-D-ribofuranosylamine
  • N(1)-(5-phospho-D-ribosyl)glycinamide
  • N1-(5-phospho-D-ribosyl)glycinamide
  • N1-(5-Phospho-beta-D-ribosyl)glycinamide
  • N1-(5-Phospho-b-D-ribosyl)glycinamide
  • N1-(5-Phospho-β-D-ribosyl)glycinamide
  • 2-Amino-N-(5-O-phosphono-beta-D-ribofuranosyl)acetamide
  • 2-Amino-N-(5-O-phosphono-β-D-ribofuranosyl)acetamide
  • 5-Phospho-beta-D-ribosyl-glycineamide
  • 5-Phospho-β-D-ribosyl-glycineamide
  • 5’-Phosphoribosylglycinamide
  • 5’-Phosphoribosylglycineamide
CAS number10074-18-7
WeightAverage: 286.1764
Monoisotopic: 286.056601978
InChI KeyOBQMLSFOUZUIOB-SHUUEZRQSA-N
InChIInChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/t3-,5-,6-,7-/m1/s1
IUPAC Name{[(2R,3S,4R,5R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Nameglycineamide ribonucleotide
Chemical FormulaC7H15N2O8P
SMILES[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP(=O)(O[H])O[H])[C@@]1([H])O[H])N([H])C(=O)C([H])([H])N([H])[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as glycinamide ribonucleotides. Glycinamide ribonucleotides are compounds in which the amide N atom of glycineamide is linked to the C-1 of a ribosyl (or deoxyribosyl) moiety. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassGlycinamide ribonucleotides
Sub ClassNot Available
Direct ParentGlycinamide ribonucleotides
Alternative Parents
Substituents
  • Glycinamide-ribonucleotide
  • Pentose phosphate
  • Pentose-5-phosphate
  • Alpha-amino acid amide
  • Alpha-amino acid or derivatives
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Monoalkyl phosphate
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetrahydrofuran
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Amino acid or derivatives
  • Carboxamide group
  • 1,2-diol
  • Organoheterocyclic compound
  • Oxacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxide
  • Primary aliphatic amine
  • Organopnictogen compound
  • Alcohol
  • Organonitrogen compound
  • Carbonyl group
  • Organooxygen compound
  • Amine
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility14.6 g/LALOGPS
logP-2.4ALOGPS
logP-4.7ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)8.14ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area171.57 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity55.29 m³·mol⁻¹ChemAxon
Polarizability23.68 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
One Carbon Pool by Folate IPW002468 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB Reactions
Tetrahydrofolic acid + 5'-Phosphoribosyl-N-formylglycinamide → N10-Formyl-THF + Glycineamideribotide
5'-phosphoribosyl-a-N-formylglycineamidine + Tetrahydrofolic acid → water + Glycineamideribotide + 5,10-Methenyltetrahydrofolic acid
KEGG Reactions
N10-Formyl-THF + Glycineamideribotide → 5,6,7,8-Tetrahydrofolic acid + hydron + 5'-Phosphoribosyl-N-formylglycinamide
Adenosine triphosphate + Glycine + 5-Phosphoribosylamine ↔ phosphate + hydron + ADP + Glycineamideribotide
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-000t-9420000000-d7fee78dd4657e2eba28JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00si-9541200000-4a23e3091baf72b01dc2JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-053i-9460000000-f71dc4d8ec0f4da03819JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0560-9120000000-4770933b45387be6728cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a59-9200000000-a6f2b9ab201fd0e69ee8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0170-9550000000-99520656892b8c415efbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-d6c860661b01956c80acJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-c2f2b85e6ec9caaa4408JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-2090000000-f6fcd99577c7e5d5d2ecJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9020000000-f5f361d4aef59382fc15JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-962cd48ee45a1c95e446JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0980000000-6a9e014a86b77c5ad3c3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5920000000-cb0c5e3520ad275d3742JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-057j-9500000000-ab2ea8c5eb8a25044810JSpectraViewer
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
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18349
HMDB IDHMDB02022
Pubchem Compound ID440137
Kegg IDC03838
ChemSpider ID141370
FOODB IDFDB022801
WikipediaGlycineamideribotide
BioCyc ID5-PHOSPHO-RIBOSYL-GLYCINEAMIDE

Enzymes

Protein Details
1. Phosphoribosylglycinamide formyltransferase
General function:
Involved in hydroxymethyl-, formyl- and related transferase activity
Specific function:
10-formyltetrahydrofolate + N(1)-(5-phospho-D- ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5- phospho-D-ribosyl)glycinamide
Gene Name:
ADE8
Uniprot ID:
P04161
Molecular weight:
23540.0
Reactions
10-formyltetrahydrofolate + N(1)-(5-phospho-D-ribosyl)glycinamide → tetrahydrofolate + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide.
Protein Details
2. Bifunctional purine biosynthetic protein ADE5,7
General function:
Involved in catalytic activity
Specific function:
ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide
Gene Name:
ADE5
Uniprot ID:
P07244
Molecular weight:
86067.39844
Reactions
ATP + 5-phospho-D-ribosylamine + glycine → ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.
ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine → ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole.
Protein Details
3. Phosphoribosylaminoimidazole carboxylase
General function:
Involved in phosphoribosylaminoimidazole carboxylase activity
Specific function:
5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxylate = 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2)
Gene Name:
ADE2
Uniprot ID:
P21264
Molecular weight:
62338.69922
Reactions
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate → 5-amino-1-(5-phospho-D-ribosyl)imidazole + CO(2).