5-Amino-6-(5-phospho-D-ribitylamino)uracil (YMDB00425)

Identification
YMDB IDYMDB00425
Name5-Amino-6-(5-phospho-D-ribitylamino)uracil
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5-Amino-6-(5'-phosphoribitylamino)uracil belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit. 5-Amino-6-(5'-phosphoribitylamino)uracil exists in all living species, ranging from bacteria to plants to humans. Based on a literature review very few articles have been published on 5-Amino-6-(5'-phosphoribitylamino)uracil.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • 5-Amino-2,6-dioxy-4-(5'-phospho-D-ribitylamino)pyrimidine
  • 5-Amino-2,6-dioxy-4-(5'-phosphoribitylamino)pyrimidine
  • 5-Amino-6-(5-phosphoribitylamino)uracil
  • 5-Amino-6-(5'-phospho-D-ribitylamino)uracil
  • 5-Amino-6-(5'-phosphoribitylamino)uracil
  • 5-Amino-6-(5-phospho-D-ribitylamino)uracil
  • 5-Amino-2,6-dioxy-4-(5’-phospho-D-ribitylamino)pyrimidine
  • 5-Amino-6-(5’-phospho-D-ribitylamino)uracil
  • 5-Amino-6-(5’-phosphoribitylamino)uracil
  • 5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione-5'-phosphate
  • 5-Amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione-5’-phosphate
CAS numberNot Available
WeightAverage: 356.2264
Monoisotopic: 356.073314674
InChI KeyRQRINYISXYAZKL-RPDRRWSUSA-N
InChIInChI=1S/C9H17N4O9P/c10-5-7(12-9(18)13-8(5)17)11-1-3(14)6(16)4(15)2-22-23(19,20)21/h3-4,6,14-16H,1-2,10H2,(H2,19,20,21)(H3,11,12,13,17,18)/t3-,4+,6-/m0/s1
IUPAC Name{[(2R,3S,4S)-5-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxy}phosphonic acid
Traditional IUPAC Name[(2R,3S,4S)-5-[(5-amino-2,6-dioxo-1,3-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxyphosphonic acid
Chemical FormulaC9H17N4O9P
SMILESNC1=C(NC[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O)NC(=O)NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharide phosphates
Alternative Parents
Substituents
  • Monosaccharide phosphate
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Secondary aliphatic/aromatic amine
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Urea
  • Secondary alcohol
  • Organoheterocyclic compound
  • Polyol
  • Azacycle
  • Secondary amine
  • Primary amine
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Alcohol
  • Organopnictogen compound
  • Amine
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility2.89 g/LALOGPS
logP-2.5ALOGPS
logP-4.5ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.49ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area223.7 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity82.36 m³·mol⁻¹ChemAxon
Polarizability30.06 ųChemAxon
Number of Rings1ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB Pathways
Riboflavin metabolismPW002443 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Riboflavin metabolismec00740 Map00740
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, Positivesplash10-000j-7932000000-f99b2e65ef6ba20ea0f8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0249000000-aad1afed0b055e36f1f2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-052f-2932000000-8ce6cdef86c0d6904216JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-9810000000-0889d500d98fdc446282JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03mi-6926000000-99084eeb27c449bf8cafJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004l-9100000000-7df2c276c4edd1cadab5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-c2c18ea089d342debbafJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0039000000-29673935259424dca664JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-052f-0490000000-f14bfba265a959aa7c3dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-6900000000-c2d4ad73928d0404741bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-8009000000-122c5a4319e344f1a64bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-77766ee562ec0704b879JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004l-9100000000-4ea49ebd63ee36be8b96JSpectraViewer
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:
  • 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
  • Richter, G., Fischer, M., Krieger, C., Eberhardt, S., Luttgen, H., Gerstenschlager, I., Bacher, A. (1997). "Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis." J Bacteriol 179:2022-2028.9068650
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18247
HMDB IDHMDB0003841
Pubchem Compound ID45266638
Kegg IDC04454
ChemSpider ID18921533
FOODB IDFDB030559
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Bifunctional protein RIB2
General function:
Involved in zinc ion binding
Specific function:
Involved in riboflavin biosynthesis. Converts 2,5- diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5- amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate
Gene Name:
RIB2
Uniprot ID:
Q12362
Molecular weight:
67035.29688
Reactions
tRNA uridine → tRNA pseudouridine.
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O → 5-amino-6-(5-phosphoribosylamino)uracil + NH(3).