GDP-4-dehydro-6-deoxy-α-D-mannose (ECMDB24242) (M2MDB006359)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2015-09-08 17:50:22 -0600
Update Date2015-09-14 16:46:44 -0600
Secondary Accession Numbers
  • ECMDB24242
Identification
Name:GDP-4-dehydro-6-deoxy-α-D-mannose
DescriptionGDP-4-dehydro-6-deoxy-alpha-D-mannose is an intermediate in GDP-L-fucose biosynthesis I (from GDP-D-mannose) in E.coli. It is a substrate for the enzyme GDP-fucose synthase which catalyzes the reaction GDP-4-dehydro-6-deoxy-alpha-D-mannose + NADPH + H+ -> GDP-beta-L-fucose + NADP+. It is also a product for enzyme GDP-mannose 4,6-dehydratase which catalyzes reaction GDP-alpha-D-mannose -> GDP-4-dehydro-6-deoxy-alpha-D-mannose + H2O (BioCYc compound: GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
ValueSource
GDP-4-Dehydro-6-deoxy-alpha-D-mannose dianionChEBI
GDP-4-Dehydro-alpha-D-rhamnoseChEBI
GDP-4-Dehydro-6-deoxy-a-D-mannose dianionGenerator
GDP-4-Dehydro-6-deoxy-α-D-mannose dianionGenerator
GDP-4-Dehydro-a-D-rhamnoseGenerator
GDP-4-Dehydro-α-D-rhamnoseGenerator
GDP-4-dehydro-6-Deoxy-a-D-mannose(2-)Generator
GDP-4-dehydro-6-Deoxy-α-D-mannose(2-)Generator
Chemical Formula:C16H21N5O15P2
Weight:Average: 585.313
Monoisotopic: 585.052036152
InChI Key:PNHLMHWWFOPQLK-BKUUWRAGSA-L
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)/p-2/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1
CAS number:Not Available
IUPAC Name:9-[(2R,3R,4S,5R)-5-{[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl phosphonato)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-2-imino-3,9-dihydro-2H-purin-6-olate
Traditional IUPAC Name:9-[(2R,3R,4S,5R)-5-[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy(hydroxy)phosphoryl phosphonato}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-2-imino-3H-purin-6-olate
SMILES:[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])O[C@]([H])(C)C(=O)[C@]([H])(O)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3[O-])[C@]([H])(O)[C@]1([H])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
  • Pyrimidone
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • Cyclic ketone
  • Ketone
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Carbonyl group
  • Organic oxygen compound
  • Organic nitrogen compound
  • Alcohol
  • Amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Primary amine
  • Organonitrogen compound
  • Organooxygen compound
  • Organic anion
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility7.65 g/LALOGPS
logP-1.4ALOGPS
logP-4.1ChemAxon
logS-1.9ALOGPS
pKa (Strongest Acidic)1.71ChemAxon
pKa (Strongest Basic)2.78ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area310.69 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity136.21 m³·mol⁻¹ChemAxon
Polarizability48.47 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Guanosine diphosphate mannose > Water + GDP-4-dehydro-6-deoxy-α-D-mannose
GDP-4-dehydro-6-deoxy-α-D-mannose + NADPH + Hydrogen ion + NADPH > NADP + GDP-β-L-fucose
SMPDB Pathways:
Amino sugar and nucleotide sugar metabolism IIPW000887 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0200090000-388df5902bd673b3f3ecView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00lr-0021090000-09b9315c6b1960463a08View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0007-9200000000-f600218625e165154ea7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001i-3200090000-60e2b5e121b22d2dc63cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-9600070000-3c1170b42c3cc3f43e7eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9100000000-3ec23c48e32bfc246243View in MoNA
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
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID57964
HMDB IDNot Available
Pubchem Compound ID25243979
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

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.