GDP-4-Dehydro-6-deoxy-D-mannose (PAMDB000347)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000347
Identification
Name: GDP-4-Dehydro-6-deoxy-D-mannose
Description:GDP-4-Dehydro-6-deoxy-D-mannose is an intermediate in fructose and mannose metabolism. GDP-4-Dehydro-6-deoxy-D-mannose is generated by GDP-D-mannose-4,6-dehydratase (GMD). This compound is then converted by the FX protein (GDP-4-keto-6-D-deoxymannose epimerase/GDP-4-keto-6-L-galactose reductase) to GDP-L-fucose. . It is also involved in amino sugar and nucleotide sugar metabolism. (KEGG)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • GDP-4-Dehydro-6-deoxy-D-mannose
  • GDP-4-Dehydro-6-deoxy-D-talose
  • GDP-4-Dehydro-D-rhamnose
  • GDP-4-Keto-6-D-deoxymannose
  • GDP-4-keto-6-deoxy-α-D-mannose
  • GDP-4-keto-6-Deoxy-a-D-mannose
  • GDP-4-Keto-6-deoxy-alpha-D-mannose
  • GDP-4-Keto-6-deoxy-D-mannose
  • GDP-4-keto-6-Deoxy-α-D-mannose
  • GDP-4-Keto-6-deoxymannose
  • GDP-4-Oxo-6-deoxy-D-mannose
  • GDP-4-Oxo-6-deoxymannose
  • Guanosine diphosphate-4-keto-6-deoxy-D-mannose
  • Guanosine diphosphoric acid-4-keto-6-deoxy-D-mannose
Chemical Formula: C16H23N5O15P2
Average Molecular Weight: 587.3258
Monoisotopic Molecular Weight: 587.066588115
InChI Key: PNHLMHWWFOPQLK-BKUUWRAGSA-N
InChI:InChI=1S/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1
CAS number: 18186-48-6
IUPAC Name:[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy})phosphinic acid
Traditional IUPAC Name: gdp-4-keto-6-deoxymannose
SMILES:C[C@H]1O[C@H](OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@@H](O)C1=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine nucleotide sugars
Direct Parent Purine nucleotide sugars
Alternative Parents
Substituents
  • Purine nucleotide sugar
  • Purine ribonucleoside diphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Hypoxanthine
  • 6-oxopurine
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Imidazole
  • Azole
  • Cyclic ketone
  • Secondary alcohol
  • Lactam
  • Ketone
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility7.05 mg/mLALOGPS
logP-1.6ALOGPS
logP-3.8ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.31ChemAxon
pKa (Strongest Basic)3.19ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area304.04 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity116.2 m3·mol-1ChemAxon
Polarizability48 Å3ChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
GDP-4-Dehydro-6-deoxy-D-mannose > GDP-4-Oxo-L-fucose
Guanosine diphosphate mannose <> GDP-4-Dehydro-6-deoxy-D-mannose + Water
GDP-L-Fucose + NADP <> GDP-4-Dehydro-6-deoxy-D-mannose + NADPH + Hydrogen ion
GDP-L-Fucose + NADP > GDP-4-Dehydro-6-deoxy-D-mannose + NADPH
GDP-4-Dehydro-6-deoxy-D-mannose + NADPH + Hydrogen ion + NADPH > GDP-L-Fucose + NADP
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0910520000-fcbc13f148251be94ff4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0910000000-ed550a57c125fee026eeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-a873b451fb06d591cb14View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f79-3901480000-ab8899450fb110bccaf6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-1901000000-c6a3e1a0d5247f947a8aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0pdl-3900000000-148e1fc1e5c7ae57395cView in MoNA
References
References:
  • 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
  • Roos, C., Kolmer, M., Mattila, P., Renkonen, R. (2002). "Composition of Drosophila melanogaster proteome involved in fucosylated glycan metabolism." J Biol Chem 277:3168-3175. Pubmed: 11698403
  • 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: Oths, Philip J.; Mayer, Robert M.; Floss, Heinz G. Stereochemistry and mechanism of the GDP-mannose dehydratase reaction. Carbohydrate Research (1990), 198(1), 91-100.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16955
HMDB IDHMDB01346
Pubchem Compound ID439446
Kegg IDC01222
ChemSpider ID388554
Wikipedia IDNot Available
BioCyc IDGDP-4-DEHYDRO-6-DEOXY-D-MANNOSE
EcoCyc IDGDP-4-DEHYDRO-6-DEOXY-D-MANNOSE