Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose (PAMDB001762)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001762
Identification
Name: Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose
Description:Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose is a member of the chemical class known as Pyrimidine Nucleotide Sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
Structure
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🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • UDP-4-Amino-4-deoxy-L-arabinose
  • Uridine 5''-diphospho-{β}-4-deoxy-4-amino-L-arabinose
Chemical Formula: C14H22N3O15P2
Average Molecular Weight: 534.2831
Monoisotopic Molecular Weight: 534.052615073
InChI Key: GWBAKYBSWHQNMQ-IAZOVDBXSA-M
InChI:InChI=1S/C14H23N3O15P2/c15-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)17-2-1-7(18)16-14(17)23/h1-2,5-6,8-13,19-22H,3-4,15H2,(H,24,25)(H,26,27)(H,16,18,23)/p-1/t5-,6+,8-,9+,10+,11+,12+,13+/m0/s1
CAS number: Not Available
IUPAC Name:1-[(2R,3R,4S,5R)-5-[({[({[(2R,3R,4S,5S)-5-amino-3,4-dihydroxyoxan-2-yl]oxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-olate
Traditional IUPAC Name: 1-[(2R,3R,4S,5R)-5-{[({[(2R,3R,4S,5S)-5-amino-3,4-dihydroxyoxan-2-yl]oxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-2-oxopyrimidin-4-olate
SMILES:[H][C@]1(COP(O)(=O)OP(O)(=O)O[C@@]2([H])OC[C@]([H])(N)[C@]([H])(O)[C@@]2([H])O)O[C@@]([H])(N2C=CC([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct Parent Pyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • 1,2-aminoalcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Amine
  • Alcohol
  • Organic anion
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-1
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility28.7 mg/mLALOGPS
logP-1.8ALOGPS
logP-5.3ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)8.84ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area283.42 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity113.02 m3·mol-1ChemAxon
Polarizability43.29 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
L-Glutamate + UDP-4-Keto-pyranose <> alpha-Ketoglutarate + Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose
N10-Formyl-THF + Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose <> Hydrogen ion + Tetrahydrofolic acid + Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose
N10-Formyl-THF + Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose <> Tetrahydrofolic acid + Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose
Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose + Oxoglutaric acid <> UDP-4-Keto-pyranose + L-Glutamate
Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose + an N10-formyl-tetrahydrofolate + N10-Formyl-THF > UDP-4-Deoxy-4-formamido-beta-L-arabinose + Hydrogen ion + a tetrahydrofolate + Tetrahydrofolic acid
UDP-β-L-threo-pentapyranos-4-ulose + L-Glutamic acid + L-Glutamate > Oxoglutaric acid + Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose
Pathways:
  • Amino sugar and nucleotide sugar metabolism pae00520
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-1300190000-f7aff4e6b5be3a1f621aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03gi-0661090000-fc326067e2de2b1ec4e0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9300000000-1a79da5f0dd44385aaa1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00ec-9000130000-dd15292d8eec7db786c6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-9100010000-4aa3abdb9bd0cbc685d2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0059-9100000000-1ec3dab2b146878d43e1View in MoNA
References
References:
  • 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
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID58708
HMDB IDNot Available
Pubchem Compound ID25201108
Kegg IDC16153
ChemSpider ID26331313
Wikipedia IDNot Available
BioCyc IDUDP-4-AMINO-4-DEOXY-L-ARABINOSE
EcoCyc IDUDP-4-AMINO-4-DEOXY-L-ARABINOSE