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2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone (M2MDB000907)

Record Information
Version2.0
Creation Date2012-05-31 14:25:15 -0600
Update Date2015-06-03 17:19:13 -0600
Secondary Accession Numbers
  • ECMDB20058
Identification
Name:2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone
Description2,5-diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone is a nucleotide analog. It is involved in cofactor biosynthesis and riboflavin biosynthesis
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2,5-Diamino-4-hydroxy-6-(5-phosphoribosylamino)pyrimidine
  • 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-(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
  • 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine
  • 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine
  • DARP
Chemical Formula:C9H16N5O8P
Weight:Average: 353.2258
Monoisotopic: 353.073649025
InChI Key:OCLCLRXKNJCOJD-UMMCILCDSA-N
InChI:InChI=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
CAS number:Not Available
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 Name:APy
SMILES:NC1=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
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
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
Reactions:
Guanosine triphosphate + 3 Water > Formic acid + Pyrophosphate +2 Hydrogen ion + 2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone
2,5-Diamino-6-(5'-phosphoribosylamino)-4-pyrimidineone + Water + Hydrogen ion > Ammonium + 5-Amino-6-(5'-phosphoribosylamino)uracil
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_6_12) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0913000000-01557e53570bef3b9be1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-1900000000-f6658717f7c349876e0bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-002f-4900000000-73f7d2c81ed2acae2ca8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f9x-5904000000-6f5576e606f7119b4f59View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-d54a3ec0ad4389b73cc4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-8eb98271bc679458e166View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0zfr-0269000000-a8de34c1ae44909c20eaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0910000000-6d7cc99373e748c7ba8dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-2900000000-cddd454d5efee7a5a260View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0fba-9003000000-153ffc1033963749c4ddView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-388039424d74347e7877View in MoNA
MSMass Spectrum (Electron Ionization)Not 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
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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID29114
HMDB IDHMDB0304044
Pubchem Compound ID439480
Kegg IDC01304
ChemSpider ID388579
Wikipedia IDNot Available
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. 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.