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Identification
YMDB IDYMDB00147
Name2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone, also known as 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate, 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. 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone exists in all living species, ranging from bacteria to plants to humans. Based on a literature review very few articles have been published on 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone.
Structure
Thumb
Synonyms
  • 2,5-Diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one
  • 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
  • 2,5-Diamino-6-hydroxy-4-(5'-phosphoribosylamino)-pyrimidine
  • N-(2,5-diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-beta-D-ribofuranosylamine
  • 2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate
  • N-(2,5-Diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-b-D-ribofuranosylamine
  • N-(2,5-Diamino-6-hydroxypyrimidin-4-yl)-5-O-phosphono-β-D-ribofuranosylamine
  • 2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphoric acid
CAS numberNot Available
WeightAverage: 353.2258
Monoisotopic: 353.073649025
InChI KeyOCLCLRXKNJCOJD-UMMCILCDSA-N
InChIInChI=1S/C9H16N5O8P/c10-3-6(13-9(11)14-7(3)17)12-8-5(16)4(15)2(22-8)1-21-23(18,19)20/h2,4-5,8,15-16H,1,10H2,(H2,18,19,20)(H4,11,12,13,14,17)/t2-,4-,5-,8-/m1/s1
IUPAC Name{[(2R,3S,4R,5R)-5-[(2,5-diamino-6-oxo-1,6-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
Traditional IUPAC NameAPy
Chemical FormulaC9H16N5O8P
SMILESNC1=NC(N[C@@H]2O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]2O)=C(N)C(O)=N1
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
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Aminopyrimidine
  • Pyrimidone
  • Secondary aliphatic/aromatic amine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Vinylogous amide
  • 1,2-diol
  • Secondary alcohol
  • Secondary amine
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Amine
  • Organic oxide
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Primary 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 Solubility5.7 g/LALOGPS
logP-2.2ALOGPS
logP-4.2ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)1.05ChemAxon
pKa (Strongest Basic)1.71ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area221.98 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity82.06 m³·mol⁻¹ChemAxon
Polarizability29.99 ųChemAxon
Number of Rings2ChemAxon
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
NADPH + hydron + 2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidineNADP + 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone
GTP + waterPyrophosphate + Formic acid + 2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_6_12) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0913000000-01557e53570bef3b9be1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-1900000000-f6658717f7c349876e0bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-002f-4900000000-73f7d2c81ed2acae2ca8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f9x-5904000000-6f5576e606f7119b4f59JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-d54a3ec0ad4389b73cc4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-8eb98271bc679458e166JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0zfr-0269000000-a8de34c1ae44909c20eaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0910000000-6d7cc99373e748c7ba8dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-2900000000-cddd454d5efee7a5a260JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fba-9003000000-153ffc1033963749c4ddJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-388039424d74347e7877JSpectraViewer
MSMass Spectrum (Electron Ionization)Not 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
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
  • 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 ID29114
HMDB IDHMDB0304044
Pubchem Compound ID439480
Kegg IDC01304
ChemSpider ID388579
FOODB IDFDB030303
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

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).
General function:
Involved in GTP cyclohydrolase II activity
Specific function:
Catalyzes the conversion of GTP to 2,5-diamino-6- ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate
Gene Name:
RIB1
Uniprot ID:
P38066
Molecular weight:
38331.60156
Reactions
GTP + 3 H(2)O → formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.
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.