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N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide (YMDB00759)

Identification
YMDB IDYMDB00759
NameN(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionN(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide, also known as 5'-phosphoribosyl-N-formylglycinamide or N-formyl-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. N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide is an extremely weak basic (essentially neutral) compound (based on its pKa). N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide exists in both E. coli (prokaryote) and yeast (eukaryote).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 5-phosphoribosyl-n-formylglycinamide
  • 5'-Phosphoribosyl-N-formylglycinamide
  • n-formyl-gar
  • n-formylglycinamide ribonucleotide
  • N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide
CAS number349-34-8
WeightAverage: 314.1865
Monoisotopic: 314.0515166
InChI KeyVDXLUNDMVKSKHO-ZRTZXPPTSA-N
InChIInChI=1S/C8H15N2O9P/c11-3-9-1-5(12)10-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H,9,11)(H,10,12)(H2,15,16,17)/t4-,6-,7-,8?/m1/s1
IUPAC Name{[(2R,3S,4R)-3,4-dihydroxy-5-(2-formamidoacetamido)oxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC NameN-Formyl-GAR
Chemical FormulaC8H15N2O9P
SMILESO[C@H]1[C@@H](O)C(NC(=O)CNC=O)O[C@@H]1COP(O)(O)=O
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
  • N-formyl-alpha amino acid or derivatives
  • Alpha-amino acid amide
  • N-formyl-alpha-amino acid
  • N-substituted-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Monosaccharide
  • Phosphoric acid ester
  • Tetrahydrofuran
  • Secondary carboxylic acid amide
  • 1,2-diol
  • Carboxamide group
  • Secondary alcohol
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility6.52 g/LALOGPS
logP-2.3ALOGPS
logP-3.9ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)-1.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area174.65 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity60.25 m³·mol⁻¹ChemAxon
Polarizability25.66 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
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
tetrahydrofolate biosynthesisPW002417 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB ReactionsNot Available
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, Positivesplash10-0002-9330000000-47bd3a51454a22349c16JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-05n0-4391000000-a2e64d6206055bba1264JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0ads-9370000000-1d426c16f66d583bca44JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9400000000-e3430b27eecb4f2388bdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01tc-9623000000-d6c1bcb3aac926c857f6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-59d3cfaf8e8cd6b90ec0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a01410784072a771fa3fJSpectraViewer
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
  • Caperelli, C. A., Chettur, G., Lin, L. Y., Benkovic, S. J. (1978). "Purfication of glycineamide ribonucleotide transformylase." Biochem Biophys Res Commun 82:403-410.666851
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18272
HMDB IDNot Available
Pubchem Compound ID45266641
Kegg IDC04376
ChemSpider ID13177010
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc ID5-P-RIBOSYL-N-FORMYLGLYCINEAMIDE

Enzymes

Protein Details
1. Phosphoribosylformylglycinamidine synthase
General function:
Involved in catalytic activity
Specific function:
ATP + N(2)-formyl-N(1)-(5-phospho-D- ribosyl)glycinamide + L-glutamine + H(2)O = ADP + phosphate + 2- (formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate
Gene Name:
ADE6
Uniprot ID:
P38972
Molecular weight:
148904.0
Reactions
ATP + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H(2)O → ADP + phosphate + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate.
Protein Details
2. 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.