Record Information
Version2.0
Creation Date2012-05-31 13:50:24 -0600
Update Date2015-06-03 15:53:56 -0600
Secondary Accession Numbers
  • ECMDB01346
Identification
Name:GDP-4-Dehydro-6-deoxy-D-mannose
DescriptionGDP-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. (PMID: 11698403). It is also involved in amino sugar and nucleotide sugar metabolism. (KEGG)
Structure
Thumb
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
Weight:Average: 587.3258
Monoisotopic: 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
Description 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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine nucleotide sugars
Direct ParentPurine nucleotide sugars
Alternative Parents
Substituents
  • Purine nucleotide sugar
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-oxopurine
  • Hypoxanthine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Pyrimidine
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Monosaccharide
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Tetrahydrofuran
  • Vinylogous amide
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Cyclic ketone
  • Secondary alcohol
  • Ketone
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Hydrocarbon derivative
  • Primary amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Alcohol
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility7.05 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity116.2 m³·mol⁻¹ChemAxon
Polarizability48 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Mannose MetabolismPW000822 ThumbThumb?image type=greyscaleThumb?image type=simple
colanic acid building blocks biosynthesisPW000951 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • GDP-L-fucose biosynthesis I (from GDP-D-mannose) PWY-66
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00mo-7594640000-f6eaffb3b87a7209c04dView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-002f-6891604000-2d6996a185dcede1dcbaView in MoNA
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

Enzymes

General function:
Involved in catalytic activity
Specific function:
Two step NADP-dependent conversion of GDP-4-dehydro-6- deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction
Gene Name:
fcl
Uniprot ID:
P32055
Molecular weight:
36141
Reactions
GDP-L-fucose + NADP(+) = GDP-4-dehydro-6-deoxy-D-mannose + NADPH.
General function:
Involved in catalytic activity
Specific function:
GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O
Gene Name:
gmd
Uniprot ID:
P0AC88
Molecular weight:
42047
Reactions
GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O.