GDP (PAMDB110473)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB110473
Identification
Name: GDP
Description:Trianion of guanosine 5'-diphosphate arising from deprotonation of the three diphosphate OH groups; major species at pH 7.3.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • ppG
  • guanosine-5'-diphosphate
  • guanosine-diphosphate
Chemical Formula: C10H12N5O11P2
Average Molecular Weight: 440.18
Monoisotopic Molecular Weight: 443.0243293706
InChI Key: QGWNDRXFNXRZMB-UUOKFMHZSA-K
InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/p-3/t3-,5-,6-,9-/m1/s1
CAS number: 146-91-8
IUPAC Name:5'-O-[(phosphonatooxy)phosphinato]guanosine
Traditional IUPAC Name: GDP
SMILES:C(OP(=O)([O-])OP(=O)([O-])[O-])C1(OC(C(O)C(O)1)N3(C=NC2(C(=O)NC(N)=NC=23)))
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Nucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
Direct Parent Purine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-oxopurine
  • Hypoxanthine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Pyrimidone
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Pyrimidine
  • Alkyl phosphate
  • N-substituted imidazole
  • Primary aromatic amine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Monosaccharide
  • Vinylogous amide
  • Heteroaromatic compound
  • Imidazole
  • Oxolane
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organic nitrogen compound
  • Amine
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility4.44 mg/mLALOGPS
logP-1.5ALOGPS
logP-3.5ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.97ChemAxon
pKa (Strongest Basic)1.35ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area248.28 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity86.37 m3·mol-1ChemAxon
Polarizability35.28 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Not Available
Reactions:
adenosylcobinamide + GTP → adenosyl-cobinamide phosphate + GDP + Hydrogen ion
pyruvate + GTP → phosphoenolpyruvate + GDP + Hydrogen ion
dGDP + Water → GDP
GTP + Water → Hydrogen ion + GDP + phosphate
GDP + ADP → GTP + AMP
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0udl-0900600000-5c7173a5771dfefadc5eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0udi-0900000000-d38af29994fa5108c331View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0udi-0900000000-3072d857dcc8a1b2cbaaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Kim HY, Thomas D, Hanley MR (1996)Stimulation of Ca(2+)-dependent membrane currents in Xenopus oocytes by microinjection of pyrimidine nucleotide-glucose conjugates. Molecular pharmacology 49, Pubmed: 8632770
  • Wennefors CK, Dobrikov MI, Xu Z, Li P, Shaw BR (2008)Stereospecificity, substrate, and inhibitory properties of nucleoside diphosphate analogs for creatine and pyruvate kinases. Bioorganic chemistry 36, Pubmed: 18433830
Synthesis Reference: Edlin, Gordon; Donini, P. Synthesis of guanosine 5'-diphosphate, 2'-(or 3'-) diphosphate, and related nucleotides in a variety of physiological conditions. Journal of Biological Chemistry (1971), 246(13), 4371-3.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CAS146-91-8
ChEBI58189
ChemSpider10239187
HMDBHMDB01201
IAF126033599
KEGGC00035
MetaboLightsMTBLC58189
PubChem21604868