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Identification
YMDB IDYMDB00898
NamedGDP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptiondGDP, also known as 2'-deoxy-GDP or 5'-dGDP, belongs to the class of organic compounds 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. dGDP is a moderately basic compound (based on its pKa). dGDP exists in all eukaryotes, ranging from yeast to humans. Within yeast, dGDP participates in a number of enzymatic reactions. In particular, dGDP can be biosynthesized from guanosine diphosphate; which is mediated by the enzyme ribonucleoside diphosphate reductase 1. In addition, dGDP can be converted into dGTP through its interaction with the enzyme nucleoside diphosphate kinase. In yeast, dGDP is involved in the metabolic pathway called purine nucleotides de novo biosynthesis pathway.
Structure
Thumb
Synonyms
  • 2'-Deoxy-GDP
  • 2'-deoxyguanosine-5'-diphosphate
  • 5'-dGDP
  • Deoxyguanosine 5'-diphosphate
  • Deoxyguanosine diphosphate
  • deoxyguanosine-diphosphate
  • dGDP
  • 2'-Deoxyguanosine 5'-diphosphate
  • 2'-Deoxyguanosine 5'-diphosphoric acid
  • Deoxyguanosine diphosphoric acid
CAS number3493-09-2
WeightAverage: 427.2011
Monoisotopic: 427.029414749
InChI KeyCIKGWCTVFSRMJU-KVQBGUIXSA-N
InChIInChI=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
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 NamedGDP
Chemical FormulaC10H15N5O10P2
SMILES[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H])N1C([H])=NC2=C1N=C(N([H])[H])N([H])C2=O
Chemical Taxonomy
Description belongs to the class of organic compounds 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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside diphosphate
  • 6-oxopurine
  • Hypoxanthine
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyrimidine
  • Heteroaromatic compound
  • Azole
  • Imidazole
  • Vinylogous amide
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary amine
  • Organic oxide
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water Solubility5.5 mg/mL [HMP experimental]PhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility3.6 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.86 m³·mol⁻¹ChemAxon
Polarizability34.99 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
purine nucleotides de novo biosynthesisPW002478 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Purine metabolismec00230 Map00230
SMPDB Reactions
dGDP + Adenosine triphosphateADP + dGTP
Guanosine diphosphate + reduced thioredoxin → oxidized thioredoxin + water + dGDP
Guanosine diphosphate + a reduced NrdH glutaredoxin-like protein → water + an oxidized NrdH glutaredoxin-like protein + dGDP
KEGG Reactions
Adenosine triphosphate + dGMPADP + dGDP
water + dGDPphosphate + hydron + dGMP
Adenosine triphosphate + dGDPADP + dGTP
water + dGTPphosphate + hydron + dGDP
thioredoxin dithiol + Guanosine diphosphate → thioredoxin disulfide + water + dGDP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Bao, J., Ryu, D. D. (2006). "Cloning of deoxynucleoside monophosphate kinase genes and biosynthesis of deoxynucleoside diphosphates." Biotechnol Bioeng 93:572-580.16240436
Synthesis Reference:Klenow, Hans; Lichtler, Eleanor; Andersen, Bjorn. Adenine deoxyriboside polyphosphates. Acta Chemica Scandinavica (1956), 10 159-60
External Links:
ResourceLink
CHEBI ID28862
HMDB IDHMDB00960
Pubchem Compound ID644
Kegg IDC00361
ChemSpider ID24785204
FOODB IDFDB022338
Wikipedia IDDeoxyguanosine_diphosphate
BioCyc IDDGDP

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
Gene Name:
RNR2
Uniprot ID:
P09938
Molecular weight:
46147.0
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage
Gene Name:
YNK1
Uniprot ID:
P36010
Molecular weight:
17166.59961
Reactions
ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.
General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
Gene Name:
RNR1
Uniprot ID:
P21524
Molecular weight:
99560.20313
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
General function:
Involved in protein binding
Specific function:
Essential for recycling GMP and indirectly, cGMP
Gene Name:
GUK1
Uniprot ID:
P15454
Molecular weight:
20637.19922
Reactions
ATP + GMP → ADP + GDP.