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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-05-12 18:41:37 UTC
HMDB IDHMDB0001346
Secondary Accession Numbers
  • HMDB01346
Metabolite Identification
Common NameGDP-4-Dehydro-6-deoxy-D-mannose
DescriptionGDP-4-Dehydro-6-deoxy-D-mannose, also known as GDP-4-dehydro-D-rhamnose or GDP-4-keto-6-deoxymannose, 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-4-Dehydro-6-deoxy-D-mannose is a strong basic compound (based on its pKa). GDP-4-Dehydro-6-deoxy-D-mannose exists in all living organisms, ranging from bacteria to humans. Within humans, GDP-4-dehydro-6-deoxy-D-mannose participates in a number of enzymatic reactions. In particular, GDP-4-dehydro-6-deoxy-D-mannose can be biosynthesized from guanosine diphosphate mannose through its interaction with the enzyme GDP-mannose 4,6 dehydratase. In addition, GDP-4-dehydro-6-deoxy-D-mannose can be biosynthesized from GDP-L-fucose through the action of the enzyme GDP-L-fucose synthase. In humans, GDP-4-dehydro-6-deoxy-D-mannose is involved in the metabolic disorder called fructosuria. Outside of the human body, GDP-4-Dehydro-6-deoxy-D-mannose has been detected, but not quantified in, several different foods, such as common walnuts, celeriacs, blackcurrants, triticales, and evergreen huckleberries. This could make GDP-4-dehydro-6-deoxy-D-mannose a potential biomarker for the consumption of these foods. A GDP-sugar having 4-dehydro-6-deoxy-alpha-D-mannose as the sugar portion.
Structure
Data?1589308897
Synonyms
ValueSource
GDP-4-Dehydro-6-deoxy-D-taloseChEBI
GDP-4-Dehydro-D-rhamnoseChEBI
GDP-4-Keto-6-deoxy-D-mannoseChEBI
GDP-4-Keto-6-deoxymannoseChEBI
GDP-4-oxo-6-Deoxy-D-mannoseChEBI
Guanosine 5'-(trihydrogen diphosphate), p'-(6-deoxy-alpha-D-lyxo-hexopyranos-4-ulos-1-yl) esterChEBI
Guanosine diphosphate-4-keto-6-deoxy-D-mannoseChEBI
GDP-4-Dehydro-alpha-D-rhamnoseKegg
GDP-4-Dehydro-6-deoxy-alpha-D-mannoseKegg
Guanosine 5'-(trihydrogen diphosphate), p'-(6-deoxy-a-D-lyxo-hexopyranos-4-ulos-1-yl) esterGenerator
Guanosine 5'-(trihydrogen diphosphate), p'-(6-deoxy-α-D-lyxo-hexopyranos-4-ulos-1-yl) esterGenerator
Guanosine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-a-D-lyxo-hexopyranos-4-ulos-1-yl) esterGenerator
Guanosine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-alpha-D-lyxo-hexopyranos-4-ulos-1-yl) esterGenerator
Guanosine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-α-D-lyxo-hexopyranos-4-ulos-1-yl) esterGenerator
Guanosine diphosphoric acid-4-keto-6-deoxy-D-mannoseGenerator
GDP-4-Dehydro-a-D-rhamnoseGenerator
GDP-4-Dehydro-α-D-rhamnoseGenerator
GDP-4-Dehydro-6-deoxy-a-D-mannoseGenerator
GDP-4-Dehydro-6-deoxy-α-D-mannoseGenerator
GDP-4-Keto-6-D-deoxymannoseHMDB
GDP-4-oxo-6-DeoxymannoseHMDB
Guanosine 5'-diphosphate 4-keto-6-deoxy-D-mannoseHMDB
Guanosine 5’-diphosphate 4-keto-6-deoxy-D-mannoseHMDB
Chemical FormulaC16H23N5O15P2
Average Molecular Weight587.3258
Monoisotopic Molecular Weight587.066588115
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 Namegdp-4-keto-6-deoxymannose
CAS Registry Number18186-48-6
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
InChI Identifier
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
InChI KeyPNHLMHWWFOPQLK-BKUUWRAGSA-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
  • 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
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility7.05 g/LALOGPS
logP-1.6ALOGPS
logP-3.6ChemAxon
logS-1.9ALOGPS
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
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00mo-7594640000-f6eaffb3b87a7209c04dSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-002f-6891604000-2d6996a185dcede1dcbaSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0910520000-fcbc13f148251be94ff4Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0910000000-ed550a57c125fee026eeSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-a873b451fb06d591cb14Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f79-3901480000-ab8899450fb110bccaf6Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-1901000000-c6a3e1a0d5247f947a8aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0pdl-3900000000-148e1fc1e5c7ae57395cSpectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022568
KNApSAcK IDC00007244
Chemspider ID388554
KEGG Compound IDC01222
BioCyc IDGDP-4-DEHYDRO-6-DEOXY-D-MANNOSE
BiGG ID37116
Wikipedia LinkNot Available
METLIN ID6180
PubChem Compound439446
PDB IDNot Available
ChEBI ID16955
Food Biomarker OntologyNot Available
VMH IDGDPDDMAN
MarkerDB ID
References
Synthesis ReferenceOths, 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
General References
  1. Roos C, Kolmer M, Mattila P, Renkonen R: Composition of Drosophila melanogaster proteome involved in fucosylated glycan metabolism. J Biol Chem. 2002 Feb 1;277(5):3168-75. Epub 2001 Nov 6. [PubMed:11698403 ]

Enzymes

General function:
Involved in catalytic activity
Specific function:
Conversion of GDP-D-mannose to GDP-4-keto-6-D-deoxymannose.
Gene Name:
GMDS
Uniprot ID:
O60547
Molecular weight:
39053.295
Reactions
Guanosine diphosphate mannose → GDP-4-Dehydro-6-deoxy-D-mannose + Waterdetails
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:
TSTA3
Uniprot ID:
Q13630
Molecular weight:
35892.46
Reactions
GDP-L-fucose + NADP → GDP-4-Dehydro-6-deoxy-D-mannose + NADPHdetails
GDP-L-fucose + NADP → GDP-4-Dehydro-6-deoxy-D-mannose + NADPH + Hydrogen Iondetails