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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'-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 is a moderately basic compound (based on its pKa). 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone exists in both E. coli (prokaryote) and yeast (eukaryote).
Structure
Thumb
MOLSDFPDBSMILESInChI
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)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
Spectrum TypeDescriptionSplash KeyView
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
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 IDFDB030303
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.