Record Information
Version2.0
Creation Date2012-10-10 12:21:46 -0600
Update Date2015-06-03 17:26:08 -0600
Secondary Accession Numbers
  • ECMDB23199
Identification
Name:UDP-4-Deoxy-4-formamido-beta-L-arabinose
DescriptionUDP-4-Deoxy-4-formamido-beta-L-arabinose is an intermediate in the polymixin resistance pathway. It is a substrate for the enzyme Bifunctional polymyxin resistance protein ArnA 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. Some Gram-negative bacteria, specifically Salmonella typhimurium and Escherichia coli, can become resistant to polymyxin by the modification of their lipid A structure via the attachment of 4-amino-4-deoxy-L-arabinopyranose (L-Ara4N) groups to one or more phosphate groups. This addition causes an absolute increase in lipid A charge, thus lowering the affinity of positively charged polymyxins.
Structure
Thumb
Synonyms:
  • (2R,3S,4R,5R)-5-(2,4-Dioxo-3,4-dihydro-1(2H)-pyrimidinyl)-3,4-dihydroxytetrahydro-2-furanylmethyl (2R,3R,4S,5S)-5-formamido-3,4-dihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferre d name)
  • (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydro-1(2H)-Pyrimidinyl)-3,4-dihydroxytetrahydro-2-furanylmethyl (2R,3R,4S,5S)-5-formamido-3,4-dihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphoric acid (non-preferre D name)
  • (2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-ylmethoxy-hydroxyphosphoryl (2R,3R,4S,5S)-5-formamido-3,4-dihydroxyoxan-2-yl hydrogen phosphate
  • (2R,3S,4R,5R)-5-(2,4-Dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-ylmethoxy-hydroxyphosphoryl (2R,3R,4S,5S)-5-formamido-3,4-dihydroxyoxan-2-yl hydrogen phosphoric acid
  • UDP-4-Deoxy-4-formamido-b-L-arabinose
  • UDP-4-Deoxy-4-formamido-β-L-arabinose
  • UDP-b-L-Ara4fn
  • UDP-beta-L-Ara4FN
  • UDP-L-Ara4FN
  • UDP-β-L-Ara4fn
  • Uridine 5'-diphospho-b-(4-deoxy-4-formamido-L-arabinose)
  • Uridine 5'-diphospho-beta-(4-deoxy-4-formamido-L-arabinose)
  • Uridine 5'-diphospho-β-(4-deoxy-4-formamido-L-arabinose)
Chemical Formula:C15H23N3O16P2
Weight:Average: 563.3011
Monoisotopic: 563.055354727
InChI Key:QGYFHZBDXXNYAX-RTXATJJPSA-N
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)/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,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-4,5-dihydroxyoxan-3-yl]carboximidic acid
Traditional IUPAC Name:udp-L-ara4FN
SMILES:[H][C@]1(COP(O)(=O)OP(O)(=O)O[C@@]2([H])OC[C@]([H])(N=CO)[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
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Urea
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Lactam
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Oxacycle
  • Organic nitrogen compound
  • Alcohol
  • Carbonyl group
  • Organonitrogen compound
  • Organooxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Organic oxygen compound
  • Hydrocarbon derivative
  • 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 Solubility10.4 g/LALOGPS
logP-1.5ALOGPS
logP-4.6ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.61ChemAxon
pKa (Strongest Basic)2.53ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area287.16 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity107.95 m³·mol⁻¹ChemAxon
Polarizability46.42 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Amino sugar and nucleotide sugar metabolism IIIPW000895 ThumbThumb?image type=greyscaleThumb?image type=simple
One Carbon Pool by Folate IPW001735 ThumbThumb?image type=greyscaleThumb?image type=simple
polymyxin resistancePW002052 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0901120000-8c46a03f73f7f398767fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3911000000-b4cab5f793e5beaf70efView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-4900000000-6d1bce8d76549b349101View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ik9-6901140000-33d8688917904f4103f1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06r6-7906010000-dffdf6a6c3314c45f1abView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06r6-5901000000-6169fa44322865858538View in MoNA
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID47027
HMDB IDNot Available
Pubchem Compound ID17756768
Kegg IDC16154
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

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.
General function:
Involved in phosphotransferase activity, for other substituted phosphate groups
Specific function:
Catalyzes the transfer of 4-deoxy-4-formamido-L- arabinose from UDP to undecaprenyl phosphate. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnC
Uniprot ID:
P77757
Molecular weight:
36339
Reactions
UDP-4-deoxy-4-formamido-beta-L-arabinose + di-trans,octa-cis-undecaprenyl phosphate = UDP + 4-deoxy-4-formamido-alpha-L-arabinose di-trans,octa-cis-undecaprenyl phosphate.