5-Phosphoribosylamine (ECMDB01128) (M2MDB000265)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (826)
Record Information
Version2.0
Creation Date2012-05-31 13:45:51 -0600
Update Date2015-09-17 15:41:09 -0600
Secondary Accession Numbers
  • ECMDB01128
Identification
Name:5-Phosphoribosylamine
Description5-Phosphoribosylamine is a substrate for Amidophosphoribosyltransferase and Trifunctional purine biosynthetic protein adenosine-3.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5-P-β-D-ribosyl-amine
  • 5-P-b-D-Ribosyl-amine
  • 5-P-b-delta-Ribosyl-amine
  • 5-P-b-δ-Ribosyl-amine
  • 5-P-beta-D-Ribosyl-amine
  • 5-P-beta-delta-Ribosyl-amine
  • 5-P-β-D-Ribosyl-amine
  • 5-P-β-δ-Ribosyl-amine
  • 5-phospho-b-D-Ribosyl-amine
  • 5-phospho-b-D-Ribosylamine
  • 5-phospho-b-delta-Ribosyl-amine
  • 5-phospho-b-delta-Ribosylamine
  • 5-phospho-b-δ-Ribosyl-amine
  • 5-phospho-b-δ-Ribosylamine
  • 5-Phospho-beta-D-ribosyl-amine
  • 5-Phospho-beta-D-ribosylamine
  • 5-Phospho-beta-delta-ribosyl-amine
  • 5-Phospho-beta-delta-ribosylamine
  • 5-Phospho-D-ribosylamine
  • 5-Phospho-delta-ribosylamine
  • 5-phospho-β-D-Ribosyl-amine
  • 5-phospho-β-D-Ribosylamine
  • 5-phospho-β-δ-Ribosyl-amine
  • 5-phospho-β-δ-Ribosylamine
  • 5-phospho-δ-Ribosylamine
  • 5-Phosphoribosylamine
  • PRA
Chemical Formula:C5H12NO7P
Weight:Average: 229.125
Monoisotopic: 229.035138255
InChI Key:SKCBPEVYGOQGJN-TXICZTDVSA-N
InChI:InChI=1S/C5H12NO7P/c6-5-4(8)3(7)2(13-5)1-12-14(9,10)11/h2-5,7-8H,1,6H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
CAS number:Not Available
IUPAC Name:{[(2R,3S,4R)-5-amino-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Name:5-phospho-D-ribosylamine
SMILES: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 pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose phosphate
  • Pentose-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetrahydrofuran
  • Secondary alcohol
  • 1,2-diol
  • Hemiaminal
  • Organoheterocyclic compound
  • Oxacycle
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Hydrocarbon derivative
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility38.2 g/LALOGPS
logP-2.4ALOGPS
logP-3.5ChemAxon
logS-0.78ALOGPS
pKa (Strongest Acidic)1.23ChemAxon
pKa (Strongest Basic)8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area142.47 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity42.49 m³·mol⁻¹ChemAxon
Polarizability18.64 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
L-Glutamine + Water + Phosphoribosyl pyrophosphate <> L-Glutamate + Pyrophosphate + 5-Phosphoribosylamine
Adenosine triphosphate + Glycine + 5-Phosphoribosylamine <> ADP + Glycineamideribotide + Hydrogen ion + Phosphate
5-Phosphoribosylamine + Pyrophosphate + L-Glutamate <> L-Glutamine + Phosphoribosyl pyrophosphate + Water
Adenosine triphosphate + 5-Phosphoribosylamine + Glycine <> ADP + Phosphate + Glycineamideribotide
5-Phosphoribosylamine + Pyrophosphate + L-Glutamate < Phosphoribosyl pyrophosphate + L-Glutamine + Water
5-Phosphoribosylamine + Pyrophosphate + L-Glutamate > L-Glutamine + Phosphoribosyl pyrophosphate + Water
Adenosine triphosphate + 5-Phosphoribosylamine + Glycine > ADP + Inorganic phosphate + 5'-Phospho-ribosylglycinamide
Phosphoribosyl pyrophosphate + Water + L-Glutamine > 5-Phosphoribosylamine + L-Glutamic acid + Pyrophosphate + 5-Phosphoribosylamine + L-Glutamate
5-Phosphoribosylamine + Glycine + Adenosine triphosphate + 5-Phosphoribosylamine > N1-(5-phospho-β-D-ribosyl)glycinamide + Phosphate + Adenosine diphosphate + Hydrogen ion + ADP
L-Glutamine + Water + Phosphoribosyl pyrophosphate <> L-Glutamate + Pyrophosphate +5 5-Phosphoribosylamine
5 5-Phosphoribosylamine + Pyrophosphate + L-Glutamate <> L-Glutamine + Phosphoribosyl pyrophosphate + Water
Adenosine triphosphate + Glycine + 5 5-Phosphoribosylamine <> ADP + Glycineamideribotide + Hydrogen ion + Phosphate
L-Glutamine + Water + Phosphoribosyl pyrophosphate <> L-Glutamate + Pyrophosphate +5 5-Phosphoribosylamine
SMPDB Pathways:
Thiamin diphosphate biosynthesisPW002028 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesisPW000910 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesis 1435709748PW000960 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesis 2PW002033 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
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-2590000000-701d3e4cccc695f0ec9fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01q9-8940000000-72b65d39cdc2ac61ecf7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0007-9100000000-a5c27bfd695bb49e9570View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-9040000000-c9c5fb67cd4a6a7824dbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a36fea1c5e53487160b1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-554f2cc279bae943d47dView in MoNA
References
References:
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID17284
HMDB IDHMDB01128
Pubchem Compound ID150
Kegg IDC03090
ChemSpider ID388939
Wikipedia5-phosphoribosylamine
BioCyc ID5-P-BETA-D-RIBOSYL-AMINE
EcoCyc ID5-P-BETA-D-RIBOSYL-AMINE

Enzymes

Protein Details
1. Amidophosphoribosyltransferase
General function:
Involved in amidophosphoribosyltransferase activity
Specific function:
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
Gene Name:
purF
Uniprot ID:
P0AG16
Molecular weight:
56488
Reactions
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O.
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.