Showing metabocard for GDP-L-fucose (BMDB0001095)

IdentificationTaxonomyPhysical propertiesSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 22:41:04 UTC
Update Date2020-06-04 18:58:18 UTC
MCDB ID BMDB0001095
Secondary Accession Numbers
  • BMDB01095
Metabolite Identification
Common NameGDP-L-fucose
DescriptionGDP-L-Fucose, also known as GDP fucose or fucose, GDP, 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. GDP-L-Fucose is possibly soluble (in water) and a moderately basic compound (based on its pKa). GDP-L-Fucose exists in all living organisms, ranging from bacteria to humans. GDP-L-Fucose participates in a number of enzymatic reactions, within cattle. In particular, GDP-L-Fucose can be converted into GDP-4-dehydro-6-deoxy-D-mannose through the action of the enzyme GDP-L-fucose synthase. In addition, GDP-L-Fucose can be biosynthesized from fucose 1-phosphate; which is mediated by the enzyme fucose-1-phosphate guanylyltransferase. In cattle, GDP-L-fucose is involved in the metabolic pathway called the fructose and mannose degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(6-Deoxy-beta-L-galactopyranosyl) esterHMDB
GDP FucoseHMDB
GDP-beta-L-FucoseHMDB
Guanosine diphosphate fucoseHMDB
Guanosine diphosphofucoseHMDB
Diphosphate fucose, guanosineHMDB
Diphosphofucose, guanosineHMDB
Fucose, GDPHMDB
Fucose, guanosine diphosphateHMDB
GDP-FucoseHMDB
GDP-Β-L-fucoseHMDB
Guanosine 5'-diphosphate L-fucoseHMDB
Guanosine 5'-diphospho-fucoseHMDB
Guanosine 5'-diphosphofucoseHMDB
Guanosine 5’-diphosphate L-fucoseHMDB
Guanosine 5’-diphospho-fucoseHMDB
Guanosine 5’-diphosphofucoseHMDB
GDP-L-fucoseHMDB
Chemical FormulaC16H25N5O15P2
Average Molecular Weight589.3417
Monoisotopic Molecular Weight589.082238179
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]({[(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid
Traditional Namegdp-L-fucose
CAS Registry Number15839-70-0
SMILES
C[C@@H]1OC(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)[C@@H]1O
InChI Identifier
InChI=1S/C16H25N5O15P2/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/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5+,7+,8+,9+,10+,11-,14+,15?/m0/s1
InChI KeyLQEBEXMHBLQMDB-QIXZNPMTSA-N
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
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetrahydrofuran
  • Vinylogous amide
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Polyol
  • Oxacycle
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Primary amine
  • Organonitrogen compound
  • Amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.7ALOGPS
logP-4.2ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area307.2 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity116.97 m³·mol⁻¹ChemAxon
Polarizability48.22 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05bf-6985780000-f2b6a0fdececb1ffd4092017-09-01View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0007-6173159000-1cf7c64a7a19bbd73e282017-10-06View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("GDP-L-fucose,1TMS,#1" TMS) - 70eV, PositiveNot Available2021-10-14View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot Available2021-10-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0910420000-6f2823064a15be7fc9a82015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0910000000-866d48af83abebf463392015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-8b884fd821ce0574d9f12015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0ukl-2801490000-f519f8992a1d7307dde62015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-1901000000-5004fbddcfb22c8ecd5f2015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0pdl-3900000000-4c564cfa5a166417a5fa2015-09-15View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0000090000-2f459a27134486d5a1ca2021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00c9-9401260000-e8773e96d7afecfae8152021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-1501900000-343d428ef047e49497952021-09-22View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0100090000-a6f771b381799c776be62021-09-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f6x-5922540000-c4c21e0fb882f03ef8632021-09-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0f7x-9740000000-e90684222b98c6e2cd5a2021-09-23View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not Available2021-09-29View Spectrum
Concentrations
StatusValueReferenceDetails
Detected and Quantified0 - 67 uM details
HMDB IDHMDB0001095
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030882
KNApSAcK IDC00007245
Chemspider ID388350
KEGG Compound IDC00325
BioCyc IDNot Available
BiGG ID34623
Wikipedia LinkNot Available
METLIN ID6001
PubChem Compound439211
PDB IDGFB
ChEBI ID17009
References
Synthesis ReferenceYamamoto, Kenji; Maruyama, Takashi; Kumagai, Hidehiko; Tochikura, Tatsurokuro; Seno, Taiko; Yamaguchi, Hideo. Preparation of GDP-L-fucose by using microbial enzymes. Agricultural and Biological Chemistry (1984), 48(3), 823-4.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Gil A, Sanchez-Medina F: Acid-soluble nucleotides of cow's, goat's and sheep's milks, at different stages of lactation. J Dairy Res. 1981 Feb;48(1):35-44. [PubMed:7196410 ]