2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine (ECMDB04052) (M2MDB000584)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (845)
Record Information
Version2.0
Creation Date2012-05-31 14:03:35 -0600
Update Date2015-06-03 15:54:41 -0600
Secondary Accession Numbers
  • ECMDB04052
Identification
Name:2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
Description2,5-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
MOLSDFPDBSMILESInChI
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
Weight:Average: 353.2258
Monoisotopic: 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
Description belongs to the class of organic compounds known as glycosylamines. Glycosylamines 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 ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Pentose monosaccharide
  • Secondary aliphatic/aromatic amine
  • Pyrimidone
  • Aminopyrimidine
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Organophosphonic acid derivative
  • Organophosphonic acid
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organophosphorus compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.36 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity92.41 m³·mol⁻¹ChemAxon
Polarizability30.01 ųChemAxon
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
Guanosine triphosphate + 3 Water > Formic acid + 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Pyrophosphate
Guanosine triphosphate + Water > 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Hydrogen ion + Formic acid + Pyrophosphate
Guanosine triphosphate + 3 Water <>2 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + Formic acid +2 Hydrogen ion + Pyrophosphate +2 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine
SMPDB Pathways:
Flavin biosynthesisPW001971 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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 ID2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
BioCyc IDDIAMINO-OH-PHOSPHORIBOSYLAMINO-PYR
EcoCyc IDDIAMINO-OH-PHOSPHORIBOSYLAMINO-PYR

Enzymes

Protein Details
1. GTP cyclohydrolase 1
General function:
Involved in GTP cyclohydrolase I activity
Specific function:
GTP + H(2)O = formate + 2-amino-4-hydroxy-6- (erythro-1,2,3-trihydroxypropyl)-dihydropteridine triphosphate
Gene Name:
folE
Uniprot ID:
P0A6T5
Molecular weight:
24830
Reactions
GTP + H(2)O = formate + 2-amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)-dihydropteridine triphosphate.
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:
ribA
Uniprot ID:
P0A7I7
Molecular weight:
21836
Reactions
GTP + 3 H(2)O = formate + 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + diphosphate.
Protein Details
3. Riboflavin biosynthesis protein ribD
General function:
Involved in zinc ion binding
Specific function:
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:
ribD
Uniprot ID:
P25539
Molecular weight:
40338
Reactions
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5-phosphoribosylamino)uracil + NH(3).
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH.