Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose (PAMDB001763)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001763
Identification
Name: Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose
Description:Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose is a member of the chemical class known as Pyrimidine Ribonucleoside Diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • UDP-β-(4-deoxy-4-formamido-L-arabinose)
  • UDP-β-L-Ara4FN
  • UDP-b-(4-Deoxy-4-formamido-L-arabinose)
  • UDP-b-L-Ara4fn
  • UDP-beta-(4-Deoxy-4-formamido-L-arabinose)
  • UDP-beta-L-Ara4FN
  • UDP-L-Ara4-Formyl-N
  • UDP-L-Ara4FN
  • UDP-β-(4-Deoxy-4-formamido-L-arabinose)
  • UDP-β-L-Ara4fn
  • Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose
Chemical Formula: C15H21N3O16P2
Average Molecular Weight: 561.2853
Monoisotopic Molecular Weight: 561.039704663
InChI Key: QGYFHZBDXXNYAX-CCMGQBSKSA-L
InChI:InChI=1S/C15H23N3O16P2/c19-5-16-6-3-30-14(12(24)9(6)21)33-36(28,29)34-35(26,27)31-4-7-10(22)11(23)13(32-7)18-2-1-8(20)17-15(18)25/h1-2,5-7,9-14,21-24H,3-4H2,(H,16,19)(H,26,27)(H,28,29)(H,17,20,25)/p-2/t6-,7+,9-,10+,11+,12+,13?,14+/m0/s1
CAS number: Not Available
IUPAC Name:N-[(3S,4S,5R,6R)-6-({[({[(2R,3S,4R)-3,4-dihydroxy-5-(4-oxido-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-4,5-dihydroxyoxan-3-yl]carboximidate
Traditional IUPAC Name: N-[(3S,4S,5R,6R)-6-[({[(2R,3S,4R)-3,4-dihydroxy-5-(4-oxido-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-4,5-dihydroxyoxan-3-yl]carboximidate
SMILES:[H][C@]1(COP(O)(=O)OP(O)(=O)O[C@@]2([H])OC[C@]([H])(N=C[O-])[C@]([H])(O)[C@@]2([H])O)OC([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
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboximidic acid derivative
  • Carboximidic acid
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic anion
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-1
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility30.5 mg/mLALOGPS
logP-1.5ALOGPS
logP-4.6ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)1.61ChemAxon
pKa (Strongest Basic)2.53ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area292.82 Å2ChemAxon
Rotatable Bond Count9ChemAxon
Refractivity129.05 m3·mol-1ChemAxon
Polarizability45.63 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Undecaprenyl phosphate + Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose > Undecaprenyl phosphate-4-amino-4-formyl-L-arabinose + Uridine 5'-diphosphate
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-formamido-L-arabinose + Di-trans,poly-cis-undecaprenyl phosphate <> Undecaprenyl phosphate alpha-L-Ara4FN + Uridine 5'-diphosphate + 4-Amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate
Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose + Di-trans,poly-cis-undecaprenyl phosphate > 4-deoxy-4-formamido-&alpha;-L-arabinopyranosyl <i>ditrans,octacis</i>-undecaprenyl phosphate + Uridine 5'-diphosphate
Pathways:
  • Amino sugar and nucleotide sugar metabolism pae00520
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0200090000-86b2795357d8f201987cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4l-0010090000-ba4510d4607fed62e983View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-074i-9600010000-f0f92eeb876e842ac15bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-9800020000-80a40303c3e3efa8bb46View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00kg-9700030000-cc2b76c71ce6d720d702View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-000x-9300000000-0e0179886b9a01c51988View 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
  • 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 ID47027
HMDB IDNot Available
Pubchem Compound ID25245185
Kegg IDC16154
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDUDP-L-ARA4-FORMYL-N
EcoCyc IDUDP-L-ARA4-FORMYL-N