Showing metabocard for GDP-4-Dehydro-6-deoxy-D-mannose (BMDB0001346)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:44:29 UTC
Update Date2020-05-21 16:28:32 UTC
BMDB IDBMDB0001346
Secondary Accession Numbers
  • BMDB01346
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 possibly soluble (in water) and 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. GDP-4-Dehydro-6-deoxy-D-mannose participates in a number of enzymatic reactions, within cattle. 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; which is mediated by the enzyme GDP-L-fucose synthase. In cattle, GDP-4-dehydro-6-deoxy-D-mannose is involved in the metabolic pathway called the fructose and mannose degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
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-1.3ALOGPS
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001346
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
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 ReferencesNot Available

Enzymes

Enzyme Details
1. dTDP-D-glucose 4,6-dehydratase
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Not Available
Gene Name:
TGDS
Uniprot ID:
A6QLW2
Molecular weight:
40666.0
Reactions
Guanosine diphosphate mannose → GDP-4-Dehydro-6-deoxy-D-mannose + Waterdetails
Enzyme Details
2. Tissue specific transplantation antigen P35B
General function:
Not Available
Specific function:
Not Available
Gene Name:
TSTA3
Uniprot ID:
Q2KIT8
Molecular weight:
36027.0
Reactions
GDP-L-fucose + NADP → GDP-4-Dehydro-6-deoxy-D-mannose + NADPHdetails