UDP-4-Deoxy-4-formamido-beta-L-arabinose (PAMDB003589)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB003589
Identification
Name: UDP-4-Deoxy-4-formamido-beta-L-arabinose
Description:UDP-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 Pseudomonas aeruginosa, 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
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🔍MOLSDFPDBSMILESInChIView Structure
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-preferred 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-preferreD 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
Average Molecular Weight: 563.3011
Monoisotopic Molecular Weight: 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
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
  • Hydroxypyrimidine
  • 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
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid derivative
  • Carboximidic acid
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • 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 Solubility10.4 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count9ChemAxon
Refractivity107.95 m3·mol-1ChemAxon
Polarizability46.42 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
N10-Formyl-THF + 4-Amino-4-deoxy-L-arabinose > Tetrahydrofolic acid + UDP-4-Deoxy-4-formamido-beta-L-arabinose
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-4-Deoxy-4-formamido-beta-L-arabinose + di-trans,octa-cis-undecaprenyl phosphate > Uridine 5'-diphosphate + 4-deoxy-4-formamido-α-L-arabinopyranosyl ditrans,octacis-undecaprenyl phosphate
Pathways: 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 ID21865444
Wikipedia IDNot Available
BioCyc IDNot Available