dTDP-D-Glucose (PAMDB000339)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000339
Identification
Name: dTDP-D-Glucose
Description:dTDP-D-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. dTDP-D-glucose is a key metabolite in prokaryotes as a precursor for a large number of modified deoxysugars, and these deoxysugars are a major part of various antibiotics, ranging from glycosides to macrolides. (PMID 18051285)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • DTDP-D-Glucose
  • DTDP-delta-glucose
  • DTDP-Glc
  • DTDP-Glucose
  • dTDP-δ-Glucose
  • DTDPglucose
  • Mono-a-D-glucopyranosyl ester
  • mono-a-delta-Glucopyranosyl ester
  • mono-a-δ-Glucopyranosyl ester
  • Mono-alpha-D-glucopyranosyl ester
  • Mono-alpha-delta-glucopyranosyl ester
  • mono-α-D-Glucopyranosyl ester
  • mono-α-δ-Glucopyranosyl ester
  • P-a-D-Glucopyranosyl ester
  • P-alpha-D-Glucopyranosyl ester
  • P-α-D-Glucopyranosyl ester
  • TDP-D-Glucose
  • TDP-delta-glucose
  • TDP-Glc
  • TDP-Glucose
  • TDP-δ-Glucose
  • TDPG
  • Thymidine 5-(trihydrogen diphosphate)
  • Thymidine 5-(trihydrogen diphosphoric acid)
  • Thymidine 5-diphosphate-D-Glucose
  • Thymidine 5-diphosphate-delta-Glucose
  • Thymidine 5-diphosphate-δ-glucose
  • Thymidine 5-diphosphoric acid-D-glucose
  • Thymidine 5-diphosphoric acid-delta-glucose
  • Thymidine 5-diphosphoric acid-δ-glucose
Chemical Formula: C16H26N2O16P2
Average Molecular Weight: 564.329
Monoisotopic Molecular Weight: 564.075755818
InChI Key: YSYKRGRSMLTJNL-KFQCIAAJSA-N
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)/t7-,8+,9+,10+,11+,12-,13+,15?/m0/s1
CAS number: 2196-62-5
IUPAC Name:{[hydroxy({[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid
Traditional IUPAC Name: dtdp-D-glucose
SMILES:CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)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
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Polyol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
LogP:-5.568PhysProp
Predicted Properties
PropertyValueSource
Water Solubility11.2 mg/mLALOGPS
logP-1.2ALOGPS
logP-3.7ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area271.31 Å2ChemAxon
Rotatable Bond Count9ChemAxon
Refractivity109.3 m3·mol-1ChemAxon
Polarizability46.61 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Thymidine 5'-triphosphate + Glucose 1-phosphate + Hydrogen ion <> dTDP-D-Glucose + Pyrophosphate
dTDP-D-Glucose <> 4,6-Dideoxy-4-oxo-dTDP-D-glucose + Water
Thymidine 5'-triphosphate + Glucose 1-phosphate <> Pyrophosphate + dTDP-D-Glucose
dTDP-D-Glucose <> dTDP-D-Galactose
dTDP-D-Glucose > dTDP-4-dehydro-6-deoxy-D-glucose + Water
Thymidine 5'-triphosphate + Hydrogen ion + Glucose 1-phosphate > Pyrophosphate + dTDP-D-Glucose
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-312a08522e3cb22b111bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-2921000000-d3da9a944bb5a8c62cfbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-415f5eced8f6fd67d535View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ik9-1403290000-6b2a8c7a42ac2eaa39c3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-4905010000-8e6b9db92566b846a800View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-4901000000-4c65036f67c107c3bdf5View in MoNA
References
References:
  • Han, J. M., Kim, S. M., Lee, H. J., Yoo, J. C. (2007). "Cloning and expression of glucose-1-phosphate thymidylyltransferase gene (schS6) from Streptomyces sp. SCC-2136." J Microbiol Biotechnol 17:685-690. Pubmed: 18051285
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Goncalves, Ruth J. Thymidine diphosphate glucose and biosynthesis of glucosides in wheat germ. I. Enzymologia (1963), 26(5), 287-93.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID15700
HMDB IDHMDB01328
Pubchem Compound ID439324
Kegg IDC00842
ChemSpider ID388455
Wikipedia IDNot Available
BioCyc IDDTDP-D-GLUCOSE
EcoCyc IDDTDP-D-GLUCOSE