GDP-4-Dehydro-6-deoxy-D-mannose (ECMDB01346) (M2MDB000347)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (408)
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
MOLSDFPDBSMILESInChI
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 Solubility6.35 g/LALOGPS
logP-1.3ALOGPS
logP-3.6ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area304.04 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity116.2 m³·mol⁻¹ChemAxon
Polarizability48.01 ųChemAxon
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 < Hydrogen ion + NADPH + GDP-4-Dehydro-6-deoxy-D-mannose
Guanosine diphosphate mannose > Water + GDP-4-Dehydro-6-deoxy-D-mannose
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
Guanosine diphosphate mannose <> GDP-4-Dehydro-6-deoxy-D-mannose + Water
Guanosine diphosphate mannose <> GDP-4-Dehydro-6-deoxy-D-mannose + Water
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 GC-MSPredicted GC-MS Spectrum - GC-MS ("GDP-4-Dehydro-6-deoxy-D-mannose,1TMS,#1" TMS) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_10) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot AvailableView in JSpectraViewer
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0000090000-45b44004cbf29fe6aa8fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-072c-7902450000-9b1901584b05fbc14f34View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-05fr-2721910000-5a19390a8eaa546bc477View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900030000-a9251fc5a1b28bbacc54View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-2911220000-4e86fd74cab914f8c823View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0zgr-9631000000-4a357d49912c73e87853View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
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

Protein Details
1. GDP-mannose 4,6-dehydratase
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.
Protein Details
2. GDP-L-fucose synthase
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.