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2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone (YMDB00424)

Identification
YMDB IDYMDB00424
Name2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone, also known as 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate, belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit. Based on a literature review very few articles have been published on 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 2,5-diamino-6-(1-D-ribitylamino)-4(3H)-Pyrimidinone 5'-phosphate
  • 2,5-diamino-6-(1-D-ribitylamino)-4(3H)-Pyrimidinone 5'-phosphoric acid
  • 2,5-diamino-6-(1-D-ribitylamino)Pyrimidin-4(3H)-one 5'-phosphate
  • 2,5-diamino-6-(1-D-ribitylamino)Pyrimidin-4(3H)-one 5'-phosphoric acid
  • 2,5-Diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one
CAS numberNot Available
WeightAverage: 355.2417
Monoisotopic: 355.089299089
InChI KeyACIVVGBVOVHFPQ-RPDRRWSUSA-N
InChIInChI=1S/C9H18N5O8P/c10-5-7(13-9(11)14-8(5)18)12-1-3(15)6(17)4(16)2-22-23(19,20)21/h3-4,6,15-17H,1-2,10H2,(H2,19,20,21)(H4,11,12,13,14,18)/t3-,4+,6-/m0/s1
IUPAC Name{[(2R,3S,4S)-5-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxy}phosphonic acid
Traditional IUPAC Name[(2R,3S,4S)-5-[(2,5-diamino-6-oxo-1H-pyrimidin-4-yl)amino]-2,3,4-trihydroxypentyl]oxyphosphonic acid
Chemical FormulaC9H18N5O8P
SMILESNC1=NC(NC[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O)=C(N)C(=O)N1
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
  • Secondary alcohol
  • Secondary amine
  • Organoheterocyclic compound
  • Polyol
  • Azacycle
  • Primary amine
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • 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 Solubility4.13 g/LALOGPS
logP-2.6ALOGPS
logP-4.9ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.49ChemAxon
pKa (Strongest Basic)6.52ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area232.98 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity84.54 m³·mol⁻¹ChemAxon
Polarizability30.98 ųChemAxon
Number of Rings1ChemAxon
Bioavailability0ChemAxon
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
Riboflavin metabolismec00740 Map00740
SMPDB ReactionsNot Available
KEGG Reactions
2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone + water + hydron → 5-Amino-6-(5'-phosphoribitylamino)uracil + Ammonium
NADPH + hydron + 2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine → NADP + 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-000e-7932000000-22e779636192f0ac701aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4r-0349000000-eb00035bf268cdd04e14JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-2932000000-94b4786f2eb398e811aeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0f6x-6910000000-cb3ff46d84f860ec7ac4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0imi-7956000000-d2aafef6cb6316df670dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9300000000-9924c8a5cf6144a3bbc6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0370eff2293c96869024JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fba-9003000000-d2a5f5778e082353a3e7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-478371c6cc802278d2f7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-ea92c5df525dcfe669e7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0029000000-ee4c9d4a5fc1cf78b04bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-052f-0390000000-f4bf9ba1d809b938dfa0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0036-7900000000-cee4cdfe318e76b20d12JSpectraViewer
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 ID52957
HMDB IDHMDB0304043
Pubchem Compound IDNot Available
Kegg IDC18910
ChemSpider ID23107011
FOODB IDFDB030302
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).
Protein Details
2. 5-amino-6-(5-phosphoribosylamino)uracil reductase
General function:
Involved in 5-amino-6-(5-phosphoribosylamino)uracil reductase activity
Specific function:
5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + NADPH
Gene Name:
RIB7
Uniprot ID:
P33312
Molecular weight:
27116.0
Reactions
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) → 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.