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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:04:23 UTC
HMDB IDHMDB01346
Secondary Accession Numbers
  • HMDB01391
Metabolite Identification
Common NameGDP-4-Dehydro-6-deoxy-D-mannose
DescriptionGDP-4-Dehydro-6-deoxy-D-mannose is an intermediate in the fucosylation of mammalian cells. The functional significance of these fucosylated glycans is unclear, although there is evidence that the sialyl Lex determinant participaates in leukocyte adhesion and trafficking processes. 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 ).
Structure
Thumb
Synonyms
ValueSource
GDP-4-dehydro-6-Deoxy-D-mannoseChEBI
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-keto-6-D-DeoxymannoseHMDB
GDP-4-oxo-6-DeoxymannoseHMDB
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 KeyInChIKey=PNHLMHWWFOPQLK-BKUUWRAGSA-N
Chemical 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.
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
  • 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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
Biofunction
  • Component of Fructose and mannose metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm (predicted from logP)
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 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
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
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid LocationsNot Available
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Fructose and Mannose DegradationSMP00064map00051
Fructose intolerance, hereditarySMP00725Not Available
FructosuriaSMP00561Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022568
KNApSAcK IDNot Available
Chemspider ID388554
KEGG Compound IDC01222
BioCyc IDGDP-4-DEHYDRO-6-DEOXY-D-MANNOSE
BiGG ID37116
Wikipedia LinkNot Available
NuGOwiki LinkHMDB01346
Metagene LinkHMDB01346
METLIN ID6180
PubChem Compound439446
PDB IDNot Available
ChEBI ID16955
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. [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