TDP-Glucose (PAMDB001135)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB001135
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
Thumb
🔍MOLSDFPDBSMILESInChIView 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 DescriptionThis 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 ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine 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
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility33.0 mg/mLALOGPS
logP-1.7ALOGPS
logP-3.3ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area280.46 Å2ChemAxon
Rotatable Bond Count9ChemAxon
Refractivity119.05 m3·mol-1ChemAxon
Polarizability45.74 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways: Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0400090000-e84ef6b94465f5199f1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0bvu-0270090000-2e01b8da2d014d64b396View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-06r5-9600000000-b5ba6089b44bf874cd03View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03dl-6200090000-82e9e1ed737dff8e65a3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-08or-9714070000-7061ef2924f2b946957cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0560-9210000000-f2da1af7f063ba4fb2e3View 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
External Links:
ResourceLink
CHEBI ID57477
HMDB IDNot Available
Pubchem Compound ID25202390
Kegg IDNot Available
ChemSpider ID26233430
Wikipedia IDNot Available
BioCyc IDDTDP-D-GLUCOSE
EcoCyc IDDTDP-D-GLUCOSE