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5-Amino-1-(5-phospho-D-ribosyl)imidazole (YMDB00492)

Identification
YMDB IDYMDB00492
Name5-Amino-1-(5-phospho-D-ribosyl)imidazole
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5-Amino-1-(5-phospho-D-ribosyl)imidazole 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. 5-Amino-1-(5-phospho-D-ribosyl)imidazole is a very strong basic compound (based on its pKa). 5-Amino-1-(5-phospho-D-ribosyl)imidazole may be a unique S. cerevisiae (yeast) metabolite.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-(5-phospho-d-ribosyl)-5-aminoimidazole
  • 1-(5-phosphoribosyl)-5-aminoimidazole
  • 1-(5'-phosphoribosyl)-5-aminoimidazole
  • 5-Amino-1-(5-phospho-D-ribosyl)imidazole
  • 5-aminoimidazole ribonucleotide
  • 5-aminoimidazole ribotide
  • 5-phosphoribosyl-5-aminoimidazole
  • 5'-phosphoribosyl-5-aminoimidazole
  • AIR
  • air, aminoimidazole ribotide
  • Aminoimidazole ribotide
CAS number25635-88-5
WeightAverage: 295.1864
Monoisotopic: 295.056936329
InChI KeyPDACUKOKVHBVHJ-ZRTZXPPTSA-N
InChIInChI=1S/C8H14N3O7P/c9-5-1-10-3-11(5)8-7(13)6(12)4(18-8)2-17-19(14,15)16/h1,3-4,6-8,12-13H,2,9H2,(H2,14,15,16)/t4-,6-,7-,8?/m1/s1
IUPAC Name{[(2R,3S,4R)-5-(5-amino-1H-imidazol-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC Nameaminoimidazole ribotide
Chemical FormulaC8H14N3O7P
SMILESNC1=CN=CN1C1O[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
  • Imidazole ribonucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Aminoimidazole
  • Alkyl phosphate
  • Phosphoric acid ester
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Heteroaromatic compound
  • Azole
  • Tetrahydrofuran
  • Imidazole
  • 1,2-diol
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxide
  • Primary amine
  • Organic nitrogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Amine
  • Organopnictogen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility3.38 g/LALOGPS
logP-2.3ALOGPS
logP-4.3ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.22ChemAxon
pKa (Strongest Basic)7.92ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area160.29 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity60.44 m³·mol⁻¹ChemAxon
Polarizability25.1 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
Thiamine metabolismec00730 Map00730
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, Positivesplash10-0002-9310000000-83cf50bc3f675ec17ccbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-9130000000-125365b6a6266dc5c7d8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-001i-9000000000-017dd2a339fc8f5491f8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-9000000000-8cfa527f76f0a0e8bc26JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0036-9160000000-92a2872e7cf8912c8f0fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0059-9000000000-818588cb1fbe6ad37863JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-57676c13a6614d36fe6dJSpectraViewer
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
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID28843
HMDB IDHMDB01235
Pubchem Compound ID161500
Kegg IDC03373
ChemSpider ID13177017
FOODB IDNot Available
Wikipedia5-amino-1-(5-phospho-D-ribosyl)imidazole
BioCyc ID5-PHOSPHORIBOSYL-5-AMINOIMIDAZOL

Enzymes

Protein Details
1. 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
2. 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).