P. aeruginosa Metabolome Database: UDP-beta-L-Threo-pentapyranos-4-ulose (PAMDB003592)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB003592

Identification

Name:

UDP-beta-L-Threo-pentapyranos-4-ulose

Description:

UDP-beta-L-Threo-pentapyranos-4-ulose is an intermediate in the polymixin resistance pathway. It is a substrate for the enzyme UDP-4-amino-4-deoxy-L-arabinose aminotransferase which catalyzes the reaction UDP-4-amino-4-deoxy-beta-L-arabinopyranose + 2-oxoglutarate = UDP-beta-L-threo-pentapyranos-4-ulose + L-glutamate. 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

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

UDP-b-L-threo-Pentapyranos-4-ulose
UDP-β-L-threo-Pentapyranos-4-ulose

Chemical Formula:

C₁₄H₂₀N₂O₁₆P₂

Average Molecular Weight:

534.2599

Monoisotopic Molecular Weight:

534.028805626

InChI Key:

URJZIQLTPCJVMW-SVROINDSSA-N

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)/t6-,8+,9-,10-,11-,12?,13-/m1/s1

CAS number:

Not Available

IUPAC Name:

{[(2R,3S,4R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}[({[(2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl)oxy]phosphinic acid

Traditional IUPAC Name:

[(2R,3S,4R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy({[(2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl]oxy(hydroxy)phosphoryl}oxy)phosphinic acid

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

Taxonomy Description

This 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 Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine 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
Heteroaromatic compound
Oxolane
Cyclic ketone
Secondary alcohol
Ketone
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	20.6 mg/mL	ALOGPS
logP	-1.2	ALOGPS
logP	-3.5	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	271.64 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	99.97 m³·mol^-1	ChemAxon
Polarizability	42.87 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

UDP-Glucuronic acid + NAD > UDP-beta-L-Threo-pentapyranos-4-ulose + Carbon dioxide + NADH

Pathways:

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0901110000-e0ba768f9204712325d7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-3910000000-66e41dd80a3d0e769bd4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-5900000000-8e25509fbca294df0a8a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03ec-5901330000-ce4dd8c67bab9e781fb7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06r6-6923000000-99667f74db4450385d6b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-06r6-5900000000-8fe9b7c43c59211f61d3	View in MoNA

References

References:

Not Available

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	25244749
Kegg ID	Not Available
ChemSpider ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available

UDP-beta-L-Threo-pentapyranos-4-ulose (PAMDB003592)

Structure for UDP-beta-L-Threo-pentapyranos-4-ulose (PAMDB003592)