dTDP-4-dehydro-6-deoxy-α-D-glucopyranose (PAMDB110410)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB110410
Identification
Name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose
Description:Dianion of dTDP-4-dehydro-6-deoxy-α-D-glucose arising from deprotonation of the diphosphate OH groups; major species at pH 7.3. It is an intermediate in dTDP-rhamnose biosynthesis.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • TDP-4-keto-6-deoxy--α-D-glucose
  • TDP-4-oxo-6-deoxy--α-D-glucose
  • dTDP-4-oxo-6-deoxy--α-D-glucose
  • dTDP-6-deoxy-α-D-xylo-4-hexosulose
  • dTDP-6-deoxy-α-D-xylohex-4-ulose
  • dTDP-4-dehydro-6-deoxy-α-D-glucose
Chemical Formula: C16H22N2O15P2
Average Molecular Weight: 544.3
Monoisotopic Molecular Weight: 546.0651911323
InChI Key: PSXWNITXWWECNY-UCBTUHGZSA-L
InChI: InChI=1S/C16H24N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-10,12-13,15,19,21-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/p-2/t7-,8+,9-,10-,12+,13-,15-/m1/s1
CAS number: Not Available
IUPAC Name:thymidine 5'-[3-(6-deoxy-α-D-xylo-hexopyranosyl-4-ulose) diphosphate]
Traditional IUPAC Name: [(3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy({hydroxy[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphoryl}oxy)phosphinic acid
SMILES:CC1(=CN(C(=O)NC(=O)1)C3(CC(O)C(COP(=O)([O-])OP(=O)([O-])OC2(OC(C)C(=O)C(O)C(O)2))O3))
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Nucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct Parent Pyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Pentose phosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Oxane
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Oxolane
  • Vinylogous amide
  • Ketone
  • Lactam
  • Secondary alcohol
  • Urea
  • Cyclic ketone
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Carbonyl group
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility11.3 mg/mLALOGPS
logP-0.93ALOGPS
logP-2ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area247.92 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity106.99 m3·mol-1ChemAxon
Polarizability45.19 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Not Available
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-5240324bf97c105ae51dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3921000000-7e9e2dfed9a99533be0aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-c718341e14191248128aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6t-3403290000-9b28f5967f6c5a9fa675View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0fbc-5904010000-e8611fa8f8e1490b7ed1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-5901000000-2158145d7f9abac6643eView in MoNA
References
References:
  • Ma Y, Mills JA, Belisle JT, Vissa V, Howell M, Bowlin K, Scherman MS, McNeil M (1997)Determination of the pathway for rhamnose biosynthesis in mycobacteria: cloning, sequencing and expression of the Mycobacterium tuberculosis gene encoding alpha-D-glucose-1-phosphate thymidylyltransferase. Microbiology (Reading, England) 143 ( Pt 3), Pubmed: 9084178
  • Ma Y, Stern RJ, Scherman MS, Vissa VD, Yan W, Jones VC, Zhang F, Franzblau SG, Lewis WH, McNeil MR (2001)Drug targeting Mycobacterium tuberculosis cell wall synthesis: genetics of dTDP-rhamnose synthetic enzymes and development of a microtiter plate-based screen for inhibitors of conversion of dTDP-glucose to dTDP-rhamnose. Antimicrobial agents and chemotherapy 45, Pubmed: 11302803
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
ChEBI57649
HMDBHMDB01399
IAF126035701
KEGGC11907
MetaboLightsMTBLC57649
PubChem25244163