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2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine (YMDB00147)

Identification
YMDB IDYMDB00147
Name2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description2,5-Diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one is an intermediate in flavin biosynthesis pathway. Riboflavin (vitamin B2) is the precursor for the essential flavin cofactors FMN and FAD, which are used in a wide variety of redox reactions. [Biocyc PWY-6168]
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
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
  • 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
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
DescriptionThis compound belongs to the class of organic compounds known as glycosylamines. These are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).
KingdomOrganic compounds
Super ClassOrganooxygen compounds
ClassCarbohydrates and carbohydrate conjugates
Sub ClassGlycosyl compounds
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Secondary aliphatic/aromatic amine
  • Aminopyrimidine
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Hydrocarbon derivative
  • Primary amine
  • 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 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)pyrimidine → NADP + 2,5-Diamino-6-(5-phosphono)ribitylamino-4(3H)-pyrimidinone
GTP + water → Pyrophosphate + Formic acid + 2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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 IDNot Available
Pubchem Compound ID439480
Kegg IDC01304
ChemSpider ID388579
FOODB IDNot Available
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. GTP cyclohydrolase-2
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.
Protein Details
3. 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.