dGDP (PAMDB120287)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB120287
Identification
Name: dGDP
Description:A 2'-deoxyribonucleoside 5'-diphosphate obtained by deprotonation of the diphosphate OH groups of dGDP.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 2'-deoxyguanosine 5'-diphosphate
  • dGDP
Chemical Formula: C10H12N5O10P2
Average Molecular Weight: 424.18
Monoisotopic Molecular Weight: 427.02942
InChI Key: CIKGWCTVFSRMJU-KVQBGUIXSA-K
InChI:InChI=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)/p-3/t4-,5+,6+/m0/s1
CAS number: 3493-09-2
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
Traditional IUPAC Name: dGDP
SMILES:C(OP(=O)([O-])OP(=O)([O-])[O-])C1(OC(CC(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 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Nucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
Direct Parent Purine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside diphosphate
  • 6-oxopurine
  • Hypoxanthine
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Azole
  • Oxolane
  • Imidazole
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Amine
  • Primary amine
  • 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 Solubility5.5 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility3.6 mg/mLALOGPS
logP-1.4ALOGPS
logP-2.6ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.97ChemAxon
pKa (Strongest Basic)1.36ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area228.05 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.86 m3·mol-1ChemAxon
Polarizability34.99 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Not Available
Reactions:
dGMP + ATP → dGDP + ADP
dGDP + Water → GDP
pyruvate + dGTP → phosphoenolpyruvate + dGDP + Hydrogen ion
dGDP + ATP → dGTP + ADP
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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
References
References:
  • Brady WA, Kokoris MS, Fitzgibbon M, Black ME: Cloning, characterization, and modeling of mouse and human guanylate kinases. J Biol Chem. 1996 Jul 12;271(28):16734-40. [8663313 ]
  • Nomanbhoy TK, Leonard DA, Manor D, Cerione RA: Investigation of the GTP-binding/GTPase cycle of Cdc42Hs using extrinsic reporter group fluorescence. Biochemistry. 1996 Apr 9;35(14):4602-8. [8605211 ]
  • Rothwell PS: The new MFGDP (UK) examination (formerly, the DGDP [UK]) Br Dent J. 1999 Oct 9;187(7):354-6. [10581811 ]
  • Bialkowski K, Kasprzak KS: Inhibition of 8-oxo-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase (8-oxo-dGTPase) activity of the antimutagenic human MTH1 protein by nucleoside 5'-diphosphates. Free Radic Biol Med. 2003 Sep 15;35(6):595-602. [12957652 ]
  • Kumar V, Spangenberg O, Konrad M: Cloning of the guanylate kinase homologues AGK-1 and AGK-2 from Arabidopsis thaliana and characterization of AGK-1. Eur J Biochem. 2000 Jan;267(2):606-15. [10632732 ]
Synthesis Reference: Klenow, Hans; Lichtler, Eleanor; Andersen, Bjorn. Adenine deoxyriboside polyphosphates. Acta Chemica Scandinavica (1956), 10 159-60
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
METABOLIGHTSMTBLC58595
HMDBHMDB00960
BIGG34741
CHEBI58595
PUBCHEM25245673
LIGAND-CPDC00361
CAS102783-74-4