GDP-4-Dehydro-6-L-deoxygalactose (PAMDB000366)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000366
Identification
Name: GDP-4-Dehydro-6-L-deoxygalactose
Description:GDP-4-dehydro-6-L-deoxygalactose is a member of the chemical class known as Purine Nucleotide Sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. GDP-6-deoxy-D-talose biosynthetic pathway involve the enzyme GDP-4-keto-6-deoxy-D-mannose-3-dehydratase, which catalyzes the third step in colitose production, which is the removal of the hydroxyl group at C3' of GDP-4-keto-6-deoxymannose. (PMID 16943443)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • GDP-4-Dehydro-6-deoxy-D-talose
  • GDP-4-Dehydro-6-L-deoxygalactose
  • GDP-4-Keto-6-deoxy-D-mannose
  • GDP-4-Keto-6-deoxymannose
  • GDP-4-Keto-6-L-deoxygalactose
  • GDP-4-Oxo-6-deoxy-D-mannose
  • GDP-4-Oxo-6-deoxymannose
  • GDP-DDMan
Chemical Formula: C16H23N5O15P2
Average Molecular Weight: 587.3258
Monoisotopic Molecular Weight: 587.066588115
InChI Key: PNHLMHWWFOPQLK-GTXIGXBOSA-N
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)/t4-,5?,8+,9+,10+,11-,14+,15?/m0/s1
CAS number: Not Available
IUPAC Name:[({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(3,4-dihydroxy-6-methyl-5-oxooxan-2-yl)oxy]phosphinic acid
Traditional IUPAC Name: {[3,4-dihydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(3,4-dihydroxy-6-methyl-5-oxooxan-2-yl)oxyphosphinic acid
SMILES:C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OCC2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@H](O)C1=O
Chemical Taxonomy
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.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine nucleotide sugars
Direct Parent Purine nucleotide sugars
Alternative Parents
Substituents
  • Purine nucleotide sugar
  • Purine ribonucleoside diphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Purine
  • Imidazopyrimidine
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Cyclic ketone
  • Secondary alcohol
  • Ketone
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility6.35 mg/mLALOGPS
logP-1.3ALOGPS
logP-3.6ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)4.94ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area305.03 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity126.78 m3·mol-1ChemAxon
Polarizability49.89 Å3ChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Guanosine diphosphate mannose > GDP-4-Dehydro-6-L-deoxygalactose + GDP-4-Dehydro-6-L-deoxygalactose
Pathways:
  • Amino sugar and nucleotide sugar metabolism pae00520
  • Fructose and mannose metabolism pae00051
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0910420000-760094d9b1806f9b8e38View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0910000000-de61a709d7ef35f70c07View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-1900000000-db427638344d393a59bfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f79-3901480000-aade95882a4e80aeb76eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-1901000000-d4665d08dec79b007630View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0pdl-3900000000-0a1076532e579915ae32View in MoNA
References
References:
  • Cook, P. D., Thoden, J. B., Holden, H. M. (2006). "The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme." Protein Sci 15:2093-2106. Pubmed: 16943443
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16955
HMDB IDHMDB01391
Pubchem Compound ID731
Kegg IDC01222
ChemSpider ID711
Wikipedia IDNot Available
BioCyc IDGDP-4-DEHYDRO-6-L-DEOXYGALACTOSE
EcoCyc IDGDP-4-DEHYDRO-6-L-DEOXYGALACTOSE