P. aeruginosa Metabolome Database: TDP-Glucose (PAMDB001135)

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

PAMDB001135

Identification

Name:

TDP-Glucose

Description:

TDP-glucose 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. Thymidine diphosphate glucose (often abbreviated dTDP-glucose or TDP-glucose) is a nucleotide-linked sugar consisting of deoxythymidine diphosphate linked to glucose. It is the starting compound for the syntheses of many deoxysugars. (WikiPedia)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

DTDP-D-Glucose
DTDP-Glucose
TDP-glucose

Chemical Formula:

C₁₆H₂₄N₂O₁₆P₂

Average Molecular Weight:

562.3131

Monoisotopic Molecular Weight:

562.060105754

InChI Key:

YSYKRGRSMLTJNL-URARBOGNSA-L

InChI:

InChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/p-2/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1

CAS number:

Not Available

IUPAC Name:

1-[(2R,4S,5R)-4-hydroxy-5-({[hydroxy({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl phosphonato]oxy}methyl)oxolan-2-yl]-5-methyl-2-oxo-1,2-dihydropyrimidin-4-olate

Traditional IUPAC Name:

1-[(2R,4S,5R)-4-hydroxy-5-[({hydroxy[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphosphoryl phosphonato}oxy)methyl]oxolan-2-yl]-5-methyl-2-oxopyrimidin-4-olate

SMILES:

[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP([O-])(=O)OP(O)(=O)O[C@@]1([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]1([H])O)N1C=C(C)C([O-])=NC1=O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine 2'-deoxyribonucleoside diphosphate
Pyrimidine deoxyribonucleotide
Organic pyrophosphate
Monosaccharide phosphate
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Organic phosphate
Monosaccharide
Hydropyrimidine
Saccharide
Heteroaromatic compound
Oxolane
Secondary alcohol
Polyol
1,2-diol
Oxacycle
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Alcohol
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nucleotide-sugar oxoanion (CHEBI:57477 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	33.0 mg/mL	ALOGPS
logP	-1.7	ALOGPS
logP	-3.3	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	280.46 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	119.05 m³·mol^-1	ChemAxon
Polarizability	45.74 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:

Pathways:

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0400090000-e84ef6b94465f5199f1f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0bvu-0270090000-2e01b8da2d014d64b396	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06r5-9600000000-b5ba6089b44bf874cd03	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03dl-6200090000-82e9e1ed737dff8e65a3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-08or-9714070000-7061ef2924f2b946957c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0560-9210000000-f2da1af7f063ba4fb2e3	View 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

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	57477
HMDB ID	Not Available
Pubchem Compound ID	25202390
Kegg ID	Not Available
ChemSpider ID	26233430
Wikipedia ID	Not Available
BioCyc ID	DTDP-D-GLUCOSE
EcoCyc ID	DTDP-D-GLUCOSE

TDP-Glucose (PAMDB001135)

Structure for TDP-Glucose (PAMDB001135)