Glycineamideribotide (ECMDB01567) (M2MDB000422)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (910)
Record Information
Version2.0
Creation Date2012-05-31 13:54:38 -0600
Update Date2015-06-03 15:54:12 -0600
Secondary Accession Numbers
  • ECMDB01567
Identification
Name:Glycineamideribotide
DescriptionGlycinamidoribotide conversion to N-formylglycinamide ribonucleotide is the third reaction of the de novo purine biosynthesis, a reaction catalyzed by the enzyme glycinamide ribonucleotide transformylase (EC 2.1.2.2). Glycinamide ribonucleotide (GAR) synthetase catalyzes the conversion of phosphoribosylamine, glycine, and MgATP to glycinamide ribonucleotide. (PMID: 2182115)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5'-p-Ribosylglycinamide
  • 5'-p-Ribosylglycineamide
  • 5'-Phosphoribosyl-glycineamide
  • 5'-Phosphoribosylglycinamide
  • 5'-Phosphoribosylglycineamide
  • GAR
  • Glycinamide ribonucleotide
  • Glycineamide ribonucleotide
  • N(1)-(5-Phospho-D-ribosyl)glycinamide
  • N-Glycyl-5-O-phosphono-D-ribofuranosylamine
  • N1-(5-phospho-D-ribosyl)glycinamide
Chemical Formula:C7H15N2O8P
Weight:Average: 286.1764
Monoisotopic: 286.056601978
InChI Key:OBQMLSFOUZUIOB-SHUUEZRQSA-N
InChI:InChI=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
CAS number:10074-18-7
IUPAC Name:{[(2R,3S,4R,5R)-5-(2-aminoacetamido)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:glycineamide ribonucleotide
SMILES:NCC(=O)N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O
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
State:Solid
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Reactions:
Adenosine triphosphate + Formic acid + Glycineamideribotide > ADP + 5'-Phosphoribosyl-N-formylglycineamide + Hydrogen ion + Phosphate
N10-Formyl-THF + Glycineamideribotide <> 5'-Phosphoribosyl-N-formylglycineamide + Hydrogen ion + Tetrahydrofolic acid
Adenosine triphosphate + Glycine + 5-Phosphoribosylamine <> ADP + Glycineamideribotide + Hydrogen ion + Phosphate
Adenosine triphosphate + 5-Phosphoribosylamine + Glycine <> ADP + Phosphate + Glycineamideribotide
N10-Formyl-THF + Glycineamideribotide <> Tetrahydrofolic acid + 5'-Phosphoribosyl-N-formylglycineamide
Glycineamideribotide + 5,10-Methenyltetrahydrofolate + Water <> 5'-Phosphoribosyl-N-formylglycineamide + Tetrahydrofolic acid
Tetrahydrofolic acid + 5'-Phosphoribosyl-N-formylglycinamide + Tetrahydrofolic acid + 5'-Phosphoribosyl-N-formylglycineamide > Water + 5,10-Methenyltetrahydrofolic acid + Glycineamideribotide + Glycineamideribotide
Tetrahydrofolic acid + 5'-Phosphoribosyl-N-formylglycinamide + Tetrahydrofolic acid + 5'-Phosphoribosyl-N-formylglycineamide > 10-Formyltetrahydrofolate + Glycineamideribotide + N10-Formyl-THF + Glycineamideribotide
5'-phosphoribosyl-a-N-formylglycineamidine + Tetrahydrofolic acid + Tetrahydrofolic acid > Water + Glycineamideribotide + 5,10-Methenyltetrahydrofolic acid + Glycineamideribotide
N10-Formyl-THF + Glycineamideribotide <>5 5'-Phosphoribosyl-N-formylglycineamide + Hydrogen ion + Tetrahydrofolic acid
Adenosine triphosphate + Glycine + 5 5-Phosphoribosylamine <> ADP + Glycineamideribotide + Hydrogen ion + Phosphate
N10-Formyl-THF + Glycineamideribotide <>5 5'-Phosphoribosyl-N-formylglycineamide + Hydrogen ion + Tetrahydrofolic acid
SMPDB Pathways:
One Carbon Pool by Folate IPW001735 ThumbThumb?image type=greyscaleThumb?image type=simple
One carbon pool by folatePW000773 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • 5-aminoimidazole ribonucleotide biosynthesis I PWY-6121
  • 5-aminoimidazole ribonucleotide biosynthesis II PWY-6122
  • superpathway of 5-aminoimidazole ribonucleotide biosynthesis PWY-6277
  • tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate PWY-6613
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-000t-9420000000-d7fee78dd4657e2eba28View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00si-9541200000-4a23e3091baf72b01dc2View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-053i-9460000000-f71dc4d8ec0f4da03819View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0560-9120000000-4770933b45387be6728cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a59-9200000000-a6f2b9ab201fd0e69ee8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0170-9550000000-99520656892b8c415efbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-d6c860661b01956c80acView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-c2f2b85e6ec9caaa4408View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-2090000000-f6fcd99577c7e5d5d2ecView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9020000000-f5f361d4aef59382fc15View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-962cd48ee45a1c95e446View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0980000000-6a9e014a86b77c5ad3c3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-5920000000-cb0c5e3520ad275d3742View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-057j-9500000000-ab2ea8c5eb8a25044810View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Caperelli CA, Giroux EL: The human glycinamide ribonucleotide transformylase domain: purification, characterization, and kinetic mechanism. Arch Biochem Biophys. 1997 May 1;341(1):98-103. Pubmed: 9143358
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • McKerns KW: Gonadotropin regulation of nucleotide biosynthesis in corpus luteum. Biochemistry. 1973 Dec 4;12(25):5206-11. Pubmed: 4366083
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID18349
HMDB IDHMDB02022
Pubchem Compound ID440137
Kegg IDC03838
ChemSpider ID141370
Wikipedia IDGlycineamide ribonucleotide
BioCyc ID5-PHOSPHO-RIBOSYL-GLYCINEAMIDE
EcoCyc ID5-PHOSPHO-RIBOSYL-GLYCINEAMIDE
Ligand ExpoGAR

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:
purN
Uniprot ID:
P08179
Molecular weight:
23238
Reactions
10-formyltetrahydrofolate + N(1)-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide.
Protein Details
2. Phosphoribosylamine--glycine ligase
General function:
Involved in ATP binding
Specific function:
ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide
Gene Name:
purD
Uniprot ID:
P15640
Molecular weight:
45940
Reactions
ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.
Protein Details
3. Phosphoribosylglycinamide formyltransferase 2
General function:
Involved in ATP binding
Specific function:
Catalyzes two reactions:the first one is the production of beta-formyl glycinamide ribonucleotide (GAR) from formate, ATP and beta GAR; the second, a side reaction, is the production of acetyl phosphate and ADP from acetate and ATP
Gene Name:
purT
Uniprot ID:
P33221
Molecular weight:
42433
Reactions
Formate + ATP + 5'-phospho-ribosylglycinamide = 5'-phosphoribosyl-N-formylglycinamide + ADP + diphosphate.