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dGDP (YMDB00898)

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 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.
Structure
Thumb
MOLSDFPDBSMILESInChI
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 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
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-2.5ChemAxon
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
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 triphosphate → ADP + 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 + dGMP ↔ ADP + dGDP
water + dGDP → phosphate + hydron + dGMP
Adenosine triphosphate + dGDP ↔ ADP + dGTP
water + dGTP → phosphate + hydron + dGDP
thioredoxin dithiol + Guanosine diphosphate → thioredoxin disulfide + water + dGDP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-056v-8931100000-80ef9c9f635e7c791ca3JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-006w-9273200000-8578b4069f91a1e37a93JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_5) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-9600800000-36eca5667f3968858676JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-0udi-2910000000-7d78949fd021bc9a3e84JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-056r-5921800000-485a79c4e3311f328cf1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-6e2fd4ae48d17fdbe9aeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000900000-f578c8db6d6baa91f146JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0udi-1900000000-eada75fb37d52199dc57JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0901100000-8f9213d3d0d12989aa4eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-fe32d673485e026f7ffdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-f9d9c2d10a52b1295c20JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0500900000-f643b08ebfbee486ac88JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-4900000000-614b7240ac447b1cf302JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-ebc82fc4fdc1243cf001JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000900000-2f685e4ebf6e3f21813bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9221200000-d3ab4261ce93db5c0d8fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900100000-b27de50984aa34aec15eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-361a2474138028086bb3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0921000000-ed51ef3ce7f119c2cbc3JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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

Protein Details
1. Ribonucleoside-diphosphate reductase small chain 1
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.
Protein Details
2. Nucleoside diphosphate kinase
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.
Protein Details
3. Ribonucleoside-diphosphate reductase large chain 1
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.
Protein Details
4. Guanylate kinase
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.