5-Amino-6-ribitylamino uracil (YMDB00171)

Identification
YMDB IDYMDB00171
Name5-Amino-6-ribitylamino uracil
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description5-Amino-6-ribitylamino uracil, also known as 4-(1-D-ribitylamino)-5-aminouracil, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 5-Amino-6-ribitylamino uracil is a strong basic compound (based on its pKa). 5-Amino-6-ribitylamino uracil exists in all living species, ranging from bacteria to humans. Within yeast, 5-amino-6-ribitylamino uracil participates in a number of enzymatic reactions. In particular, 1-deoxy-L-glycero-tetrulose 4-phosphate and 5-amino-6-ribitylamino uracil can be converted into 6,7-dimethyl-8-(D-ribityl)lumazine; which is mediated by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. In addition, riboflavin and 5-amino-6-ribitylamino uracil can be biosynthesized from 6,7-dimethyl-8-(D-ribityl)lumazine through the action of the enzyme riboflavin synthase. In yeast, 5-amino-6-ribitylamino uracil is involved in the metabolic pathway called the riboflavin metabolism pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1-[(5-amino-2,6-dihydroxypyrimidin-4-yl)amino]-1-deoxy-D-ribitol
  • 1-[(5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-1-deoxy-D-ribitol
  • 4-(1-D-Ribitylamino)-5-amino-2,6 dihydroxypyrimidine
  • 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
  • 4-(1-D-Ribitylamino)-5-aminouracil
  • 5-amino-6-(2,3,4,5-tetrahydroxypentylamino)-1H-pyrimidine-2,4-dione
  • 6-Ribitylamino-5-aminouracil
CAS numberNot Available
WeightAverage: 276.2465
Monoisotopic: 276.106984264
InChI KeyXKQZIXVJVUPORE-UHFFFAOYSA-N
InChIInChI=1S/C9H16N4O6/c10-5-7(12-9(19)13-8(5)18)11-1-3(15)6(17)4(16)2-14/h3-4,6,14-17H,1-2,10H2,(H3,11,12,13,18,19)
IUPAC Name5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name5-amino-6-[(2,3,4,5-tetrahydroxypentyl)amino]-1,3-dihydropyrimidine-2,4-dione
Chemical FormulaC9H16N4O6
SMILES[H]OC([H])([H])C([H])(O[H])C([H])(O[H])C([H])(O[H])C([H])([H])N([H])C1=C(N([H])[H])C(=O)N([H])C(=O)N1[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Aminopyrimidine
  • Pyrimidone
  • Secondary aliphatic/aromatic amine
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Urea
  • Secondary alcohol
  • Polyol
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Primary alcohol
  • Alcohol
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Amine
  • Organic nitrogen 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 Solubility14.3 g/LALOGPS
logP-2.4ALOGPS
logP-4.4ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)9.41ChemAxon
pKa (Strongest Basic)4.36ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area177.17 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity71.48 m³·mol⁻¹ChemAxon
Polarizability25.92 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
Riboflavin metabolismPW002443 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Methane metabolismec00680 Map00680
Riboflavin metabolismec00740 Map00740
SMPDB Reactions
2-Hydroxy-3-oxobutyl phosphate + 5-Amino-6-ribitylamino uracil → 6,7-Dimethyl-8-(1-D-ribityl)lumazine
6,7-Dimethyl-8-(1-D-ribityl)lumazine → Riboflavin + 5-Amino-6-ribitylamino uracil
KEGG Reactions
water + 5-Amino-6-(5'-phosphoribitylamino)uracil → 5-Amino-6-ribitylamino uracil + phosphate
5-Amino-6-ribitylamino uracil + 2-Hydroxy-3-oxobutyl phosphate → water + 6,7-Dimethyl-8-(1-D-ribityl)lumazine + phosphate
6,7-Dimethyl-8-(1-D-ribityl)lumazine → Riboflavin + 5-Amino-6-ribitylamino uracil
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0903-9440000000-d4b6a6cff43cc761315fJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-056r-6294350000-61d4d076b5309ed14bcbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-056r-1190000000-2514b630f375b2189bfeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-08fu-9750000000-779ce19c1a0e6b0c6932JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9300000000-2f9fc8d8f57a4b3ca8c6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01x0-5490000000-40e672b419cf2a89e723JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9210000000-e4e8a4b406ad4dfd459fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9200000000-0e769fc743b8cee3b542JSpectraViewer
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:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15934
HMDB IDHMDB11106
Pubchem Compound ID221
Kegg IDC04732
ChemSpider ID216
FOODB IDFDB027889
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. 6,7-dimethyl-8-ribityllumazine synthase
General function:
Involved in riboflavin biosynthetic process
Specific function:
Condensation of 5-amino-6-(1'-D)-ribityl-amino- 2,4(1H,3H)-pyrimidinedione with L-3,4-dihydroxy-2-butanone 4- phosphate to produce 6,7-dimethyl-8-(1-D-ribityl)lumazine
Gene Name:
RIB4
Uniprot ID:
P50861
Molecular weight:
18555.40039
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine → riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.
Protein Details
2. Riboflavin synthase alpha chain
General function:
Involved in riboflavin synthase activity
Specific function:
2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine
Gene Name:
RIB5
Uniprot ID:
P38145
Molecular weight:
26195.59961
Reactions
2 6,7-dimethyl-8-(1-D-ribityl)lumazine → riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine.