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Showing Compound dGDP (FDB022338)

Record Information
Version1.0
Creation date2011-09-21 00:12:25 UTC
Update date2020-09-17 15:38:45 UTC
Primary IDFDB022338
Secondary Accession NumbersNot Available
Chemical Information
FooDB NamedGDP
DescriptiondGDP, also known as 2'-deoxy-GDP or 5'-dGDP, belongs to the class of organic compounds known as hydroxycinnamic acids. Hydroxycinnamic acids are compounds containing an cinnamic acid where the benzene ring is hydroxylated. dGDP is a moderately basic compound (based on its pKa). dGDP exists in all eukaryotes, ranging from yeast to humans. Within humans, dGDP participates in a number of enzymatic reactions. In particular, dGDP can be converted into dGTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In addition, dGDP can be biosynthesized from 2'-deoxyguanosine 5'-monophosphate through its interaction with the enzyme guanylate kinase. In humans, dGDP is involved in the metabolic disorder called the gout or kelley-seegmiller syndrome pathway. Outside of the human body, dGDP has been detected, but not quantified in, several different foods, such as chinese bayberries, thistles, french plantains, nopals, and pepper (capsicum). This could make dGDP a potential biomarker for the consumption of these foods. A purine 2'-deoxyribonucleoside 5'-diphosphate having guanine as the nucleobase.
CAS Number3493-09-2
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
Predicted Properties
PropertyValueSource
Water Solubility3.6 g/LALOGPS
logP-1.4ALOGPS
logP-2.5ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.79ChemAxon
pKa (Strongest Basic)0.44ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area228.05 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.86 m³·mol⁻¹ChemAxon
Polarizability34.99 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Chemical FormulaC10H15N5O10P2
IUPAC name[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
InChI IdentifierInChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChI KeyCIKGWCTVFSRMJU-KVQBGUIXSA-N
Isomeric SMILESNC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1
Average Molecular Weight427.2011
Monoisotopic Molecular Weight427.029414749
Classification
Description Belongs to the class of organic compounds known as hydroxycinnamic acids. Hydroxycinnamic acids are compounds containing an cinnamic acid where the benzene ring is hydroxylated.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCinnamic acids and derivatives
Sub ClassHydroxycinnamic acids and derivatives
Direct ParentHydroxycinnamic acids
Alternative Parents
Substituents
  • Cinnamic acid
  • Coumaric acid or derivatives
  • Hydroxycinnamic acid
  • Methoxyphenol
  • Phenoxy compound
  • Anisole
  • Methoxybenzene
  • Styrene
  • Phenol ether
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Alkyl aryl ether
  • Phenol
  • Monocyclic benzene moiety
  • Benzenoid
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Ether
  • Organic oxygen compound
  • Carbonyl group
  • Organic oxide
  • Organooxygen compound
  • Hydrocarbon derivative
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Biological location:

Source:

Role

Industrial application:

Physico-Chemical Properties
Physico-Chemical Properties - Experimental
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSdGDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-056v-8931100000-80ef9c9f635e7c791ca3Spectrum
Predicted GC-MSdGDP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-006w-9273200000-8578b4069f91a1e37a93Spectrum
Predicted GC-MSdGDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TMS_1_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TBDMS_1_4, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdGDP, TBDMS_1_5, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-9600800000-36eca5667f39688586762017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - , positivesplash10-0udi-2910000000-7d78949fd021bc9a3e842017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-056r-5921800000-485a79c4e3311f328cf12021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-6e2fd4ae48d17fdbe9ae2021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000900000-f578c8db6d6baa91f1462021-09-20View Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0udi-1900000000-eada75fb37d52199dc572021-09-20View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0901100000-8f9213d3d0d12989aa4e2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-fe32d673485e026f7ffd2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-f9d9c2d10a52b1295c202016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0500900000-f643b08ebfbee486ac882016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-4900000000-614b7240ac447b1cf3022016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-ebc82fc4fdc1243cf0012016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000900000-2f685e4ebf6e3f21813b2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9221200000-d3ab4261ce93db5c0d8f2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1f2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900100000-b27de50984aa34aec15e2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-361a2474138028086bb32021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0921000000-ed51ef3ce7f119c2cbc32021-09-22View Spectrum
NMRNot Available
ChemSpider ID388359
ChEMBL IDNot Available
KEGG Compound IDC00361
Pubchem Compound ID439220
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB00960
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID34741
KNApSAcK IDNot Available
HET IDDGI
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
Processing...
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
Pathways
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference