2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine (PAMDB000584)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000584
Identification
Name: 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
Description:2,5-Diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine or DARP, is an intermediate in flavin biosynthesis. It is a substrate for diaminohydroxyphosphoribosylaminopyrimidine deaminase, which catalyzes the reaction 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + H2O = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH3
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 2,5-Diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate
  • 2,5-diamino-6-(1-D-ribosylamino)Pyrimidin-4(3H)-one 5'-phosphoric acid
  • 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone
  • 2,5-Diamino-6-(D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate
  • 2,5-diamino-6-(D-ribosylamino)Pyrimidin-4(3H)-one 5'-phosphoric acid
  • 2,5-Diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate
  • 2,5-Diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphoric acid
  • 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
  • 2,5DA6RA4P5P
  • DARP
Chemical Formula: C9H16N5O8P
Average Molecular Weight: 353.2258
Monoisotopic Molecular Weight: 353.073649025
InChI Key: CIEXRWBOBYOQGW-DOAYSINJSA-N
InChI:InChI=1S/C9H16N5O8P/c10-1-5(13-9(11)14-6(1)17)12-7-3(16)2(15)4(22-7)8(18)23(19,20)21/h2-4,7-8,15-16,18H,10H2,(H2,19,20,21)(H4,11,12,13,14,17)/t2-,3+,4-,7?,8?/m0/s1
CAS number: Not Available
IUPAC Name:{[(2S,3S,4R)-5-[(5-amino-6-hydroxy-2-imino-2,3-dihydropyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl](hydroxy)methyl}phosphonic acid
Traditional IUPAC Name: [(2S,3S,4R)-5-[(5-amino-6-hydroxy-2-imino-3H-pyrimidin-4-yl)amino]-3,4-dihydroxyoxolan-2-yl](hydroxy)methylphosphonic acid
SMILES:[H]C(O)([C@@]1([H])OC([H])(NC2=C(N)C(O)=NC(=N)N2)[C@]([H])(O)[C@]1([H])O)P(O)(O)=O
Chemical Taxonomy
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).
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassGlycosyl compounds
Direct Parent Glycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Hydroxypyrimidine
  • Secondary aliphatic/aromatic amine
  • Aminopyrimidine
  • Pyrimidine
  • Primary aromatic amine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Organophosphonic acid derivative
  • Organophosphonic acid
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Hydrocarbon derivative
  • Primary amine
  • Organophosphorus compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:0
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.36 mg/mLALOGPS
logP-2.6ALOGPS
logP-4.4ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.25ChemAxon
pKa (Strongest Basic)21.89ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area233.97 Å2ChemAxon
Rotatable Bond Count4ChemAxon
Refractivity92.41 m3·mol-1ChemAxon
Polarizability30.01 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Hydrogen ion + Water > 5-Amino-6-(5'-phosphoribosylamino)uracil + Ammonium
Guanosine triphosphate + 3 Water <> 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Formic acid +2 Hydrogen ion + Pyrophosphate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine
Guanosine triphosphate + 3 Water <> Formic acid + 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Pyrophosphate
2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Water + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine <> 5-Amino-6-(5'-phosphoribosylamino)uracil + Ammonia
Water + Guanosine triphosphate > Hydrogen ion + Pyrophosphate + 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Formic acid
Water + 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine > 5-Amino-6-(5'-phosphoribosylamino)uracil + Ammonia
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0903000000-d54583fd9a311884312fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-3900000000-53208a77172da4a83d20View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-002f-3900000000-612947fc7c218d0e9df5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f7o-4914000000-54a4bb0b18b52d646bf8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000x-9521000000-806330d4617413a810b5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001l-9400000000-4b19cb6e4b769db39582View in MoNA
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID29114
HMDB IDNot Available
Pubchem Compound ID25244331
Kegg IDC01304
ChemSpider ID26331269
Wikipedia IDNot Available
BioCyc IDDIAMINO-OH-PHOSPHORIBOSYLAMINO-PYR
EcoCyc IDDIAMINO-OH-PHOSPHORIBOSYLAMINO-PYR