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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 is an intermediate in flavin biosynthesis pathway. [Biocyc RIBOSYN2-PWY]
Structure
Thumb
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
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
DescriptionThis compound belongs to the class of organic compounds known as pyrimidones. These are compounds that contain a pyrimidine ring,which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Monoalkyl phosphate
  • Secondary aliphatic/aromatic amine
  • Pyrimidone
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Secondary alcohol
  • Polyol
  • Lactam
  • 1,2-diol
  • Azacycle
  • Secondary amine
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen 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-2.5ALOGPS
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 + hydron5-Amino-6-(5'-phosphoribitylamino)uracil + Ammonium
NADPH + hydron + 2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidineNADP + 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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 IDNot Available
Pubchem Compound ID25271619
Kegg IDC18910
ChemSpider ID23107011
FOODB IDNot Available
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 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.