Record Information
Version 1.0
Update Date 1/22/2018 12:54:53 PM
Metabolite IDPAMDB000209
Identification
Name: dGDP
Description:Deoxyguanosine diphosphate or dGDP is a member of the chemical class known as Purine 2'-deoxyribonucleoside Diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. DGDP is invovled in Purine metabolism. It is related to the common nucleic acid GTP, or guanosine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than GTP.
Structure
Thumb
Synonyms:
  • 2'-Deoxy-GDP
  • 2'-Deoxyguanosine-5'-diphosphate
  • 2'-Deoxyguanosine-5'-diphosphoric acid
  • 5'-dGDP
  • Deoxyguanosine 5'-diphosphate
  • Deoxyguanosine 5'-diphosphoric acid
  • Deoxyguanosine diphosphate
  • Deoxyguanosine diphosphoric acid
  • Deoxyguanosine-diphosphate
  • Deoxyguanosine-diphosphoric acid
  • DGDP
Chemical Formula: C10H15N5O10P2
Average Molecular Weight: 427.2011
Monoisotopic Molecular Weight: 427.029414749
InChI Key: CIKGWCTVFSRMJU-KVQBGUIXSA-N
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)/t4-,5+,6+/m0/s1
CAS number: 102783-74-4
IUPAC Name:[({[5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name: deoxyguanosine diphosphate
SMILES:NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O2)C(=O)N1
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Purine nucleotides
Sub ClassPurine ribonucleotides
Direct Parent Purine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Organic pyrophosphate
  • Purine
  • Imidazopyrimidine
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Heteroaromatic compound
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility3.37 mg/mLALOGPS
logP-1.4ALOGPS
logP-2.8ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.71ChemAxon
pKa (Strongest Basic)2.57ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area228.05 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.42 m3·mol-1ChemAxon
Polarizability34.81 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways: Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900100000-f4f358dc2b1e20a9159cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-fcba058e2b2acaf94cb5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-fa3b18c6714fdc0ddea3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0501900000-fe840a4cd42c2a9f01a0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-6900000000-308b2de7e3fc1a9a2ea0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-bbde619c06d1a440bbe8View in MoNA
References
References:
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDHMDB00960
Pubchem Compound ID644
Kegg IDC00361
ChemSpider ID624
Wikipedia IDDeoxyguanosine diphosphate
BioCyc IDDGDP
EcoCyc IDDGDP

Enzymes

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. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
Gene Name:
nrdA
Locus Tag:
PA1156
Molecular weight:
107.1 kDa
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
Gene Name:
ndk
Locus Tag:
PA3807
Molecular weight:
15.6 kDa
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in magnesium ion binding
Specific function:
ATP + pyruvate = ADP + phosphoenolpyruvate
Gene Name:
pykF
Locus Tag:
PA1498
Molecular weight:
51.5 kDa
Reactions
ATP + pyruvate = ADP + phosphoenolpyruvate.
General function:
Involved in magnesium ion binding
Specific function:
ATP + pyruvate = ADP + phosphoenolpyruvate
Gene Name:
pykA
Locus Tag:
PA4329
Molecular weight:
52.3 kDa
Reactions
ATP + pyruvate = ADP + phosphoenolpyruvate.
General function:
Involved in catalytic activity
Specific function:
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin
Gene Name:
nrdD
Locus Tag:
PA1920
Molecular weight:
76.1 kDa
Reactions
2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.
General function:
Involved in protein binding
Specific function:
Essential for recycling GMP and indirectly, cGMP
Gene Name:
gmk
Locus Tag:
PA5336
Molecular weight:
23.1 kDa
Reactions
ATP + GMP = ADP + GDP.
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Locus Tag:
PA3686
Molecular weight:
23.1 kDa
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
Gene Name:
nrdB
Locus Tag:
PA1155
Molecular weight:
47.4 kDa
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in electron carrier activity
Specific function:
Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
Gene Name:
grxD
Locus Tag:
PA3533
Molecular weight:
11.8 kDa
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxC
Locus Tag:
PA5129
Molecular weight:
9.2 kDa
General function:
Involved in electron carrier activity
Specific function:
Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions
Gene Name:
trxA
Locus Tag:
PA5240
Molecular weight:
11.9 kDa