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Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose (M2MDB001762)

Record Information
Version2.0
Creation Date2012-07-30 14:55:30 -0600
Update Date2015-06-03 17:21:14 -0600
Secondary Accession Numbers
  • ECMDB21366
Identification
Name:Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose
DescriptionUridine 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
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • UDP-4-Amino-4-deoxy-L-arabinose
  • Uridine 5''-diphospho-{β}-4-deoxy-4-amino-L-arabinose
Chemical Formula:C14H22N3O15P2
Weight:Average: 534.2831
Monoisotopic: 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
Description belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Secondary alcohol
  • Urea
  • Lactam
  • 1,2-aminoalcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Primary amine
  • Amine
  • Organonitrogen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Primary aliphatic amine
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organic anion
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility28.7 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity113.02 m³·mol⁻¹ChemAxon
Polarizability43.29 ųChemAxon
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 + N10-Formyl-THF > Hydrogen ion + Uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose + Tetrahydrofolic acid
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
L-Glutamate + UDP-4-Keto-pyranose <> alpha-Ketoglutarate + Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose
SMPDB Pathways:
Amino sugar and nucleotide sugar metabolism IIIPW000895 ThumbThumb?image type=greyscaleThumb?image type=simple
polymyxin resistancePW002052 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Amino sugar and nucleotide sugar metabolism ec00520
EcoCyc Pathways:
Concentrations
Not Available
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

Enzymes

Protein Details
1. Bifunctional polymyxin resistance protein ArnA
General function:
Involved in hydroxymethyl-, formyl- and related transferase activity
Specific function:
Bifunctional enzyme that catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto- arabinose (UDP-Ara4O) and the addition of a formyl group to UDP-4- amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido- arabinose (UDP-L-Ara4FN). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnA
Uniprot ID:
P77398
Molecular weight:
74288
Reactions
UDP-alpha-D-glucuronate + NAD(+) = UDP-beta-L-threo-pentapyranos-4-ulose + CO(2) + NADH.
10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinose.
Protein Details
2. UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase
General function:
Involved in transaminase activity
Specific function:
Catalyzes the conversion of UDP-4-keto-arabinose (UDP- Ara4O) to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N). The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnB
Uniprot ID:
P77690
Molecular weight:
41649
Reactions
UDP-4-amino-4-deoxy-beta-L-arabinose + 2-oxoglutarate = UDP-beta-L-threo-pentapyranos-4-ulose + glutamate.