UDP-4-Keto-pyranose (ECMDB21293) (M2MDB001697)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (37)
Record Information
Version2.0
Creation Date2012-07-30 14:55:15 -0600
Update Date2015-06-03 17:21:06 -0600
Secondary Accession Numbers
  • ECMDB21293
Identification
Name:UDP-4-Keto-pyranose
DescriptionUDP-4-keto-pyranose 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
MOLSDFPDBSMILESInChI
Synonyms:
  • UDP-4-keto-pyranose
  • UDP-4-Ketopentose
  • UDP-Ara4O
  • UDP-L-Ara4O
  • Uridine 5'-β-L-threo-pentapyranosyl-4''-ulose diphosphate
  • Uridine 5'-β-L-threo-pentapyranosyl-4''-ulose diphosphoric acid
  • Uridine 5'-b-L-threo-pentapyranosyl-4''-ulose diphosphate
  • Uridine 5'-b-L-threo-pentapyranosyl-4''-ulose diphosphoric acid
  • Uridine 5'-beta-L-threo-pentapyranosyl-4''-ulose diphosphate
  • Uridine 5'-beta-L-threo-pentapyranosyl-4''-ulose diphosphoric acid
  • Uridine 5'-β-L-threo-pentapyranosyl-4''-ulose diphosphate
  • Uridine 5'-β-L-threo-pentapyranosyl-4''-ulose diphosphoric acid
Chemical Formula:C14H18N2O16P2
Weight:Average: 532.244
Monoisotopic: 532.013155562
InChI Key:URJZIQLTPCJVMW-SVROINDSSA-L
InChI:InChI=1S/C14H20N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,6,8-13,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/p-2/t6-,8+,9-,10-,11-,12?,13-/m1/s1
CAS number:Not Available
IUPAC Name:1-[(3R,4S,5R)-5-{[({[(2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl phosphonato)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-olate
Traditional IUPAC Name:1-[(3R,4S,5R)-5-[({[(2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl]oxy(hydroxy)phosphoryl phosphonato}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])OCC(=O)[C@]([H])(O)[C@@]2([H])O)OC([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-5-phosphate
  • Pentose phosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Cyclic ketone
  • Urea
  • Secondary alcohol
  • Lactam
  • Ketone
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Organic anion
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility50.8 g/LALOGPS
logP-1.3ALOGPS
logP-3.5ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area277.3 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity109.4 m³·mol⁻¹ChemAxon
Polarizability42.18 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
NAD + Uridine diphosphate glucuronic acid > Carbon dioxide + NADH + UDP-4-Keto-pyranose
Uridine diphosphate glucuronic acid + NAD <> UDP-4-Keto-pyranose + Carbon dioxide + NADH + Hydrogen ion
Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose + Oxoglutaric acid <> UDP-4-Keto-pyranose + L-Glutamate
L-Glutamate + UDP-4-Keto-pyranose <> alpha-Ketoglutarate + Uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose
NAD + Uridine diphosphate glucuronic acid > Carbon dioxide + NADH + UDP-4-Keto-pyranose
NAD + Uridine diphosphate glucuronic acid > Carbon dioxide + NADH + UDP-4-Keto-pyranose
SMPDB Pathways:Not Available
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, Positivesplash10-001i-0200190000-d590a1d321f92c78316fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01t9-0111090000-c63a25ccd6ed116d50d3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0089-9801000000-a06ed8c72e1e5e635698View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001l-8200190000-c3435a8aa4d3d5a746bdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-003s-8900080000-05ab55bc9c02e1ebbf87View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-059x-9100000000-9c2450446a73c43177afView 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 IDNot Available
HMDB IDNot Available
Pubchem Compound ID25244748
Kegg IDC16155
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc ID5-BETA-L-THREO-PENTAPYRANOSYL-4-ULOSE-
EcoCyc ID5-BETA-L-THREO-PENTAPYRANOSYL-4-ULOSE-

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.