Record Information
Version 1.0
Update Date 1/22/2018 12:54:53 PM
Metabolite IDPAMDB000296
Identification
Name: Guanosine diphosphate
Description:Guanosine 5'-(trihydrogen diphosphate). A guanine nucleotide containing two phosphate groups esterified to the sugar moiety. It is an ester of pyrophosphoric acid with the nucleoside guanosine. GDP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase guanine. GDP is the product of GTP dephosphorylation by GTPases, e.g. the G-proteins that are involved in signal transduction.
Structure
Thumb
Synonyms:
  • 5'-GDP
  • GDP
  • Guanosine 5'-(trihydrogen pyrophosphate)
  • Guanosine 5'-(trihydrogen pyrophosphoric acid)
  • Guanosine 5'-diphosphate
  • Guanosine 5'-diphosphoric acid
  • Guanosine 5'-pyrophosphate
  • Guanosine 5'-pyrophosphoric acid
  • Guanosine diphosphoric acid
  • Guanosine mono(trihydrogen diphosphate)
  • Guanosine mono(trihydrogen diphosphoric acid)
  • Guanosine pyrophosphate
  • Guanosine pyrophosphoric acid
  • Guanosine-5'-diphosphate
  • Guanosine-5'-diphosphoric acid
  • Guanosine-diphosphate
  • Guanosine-diphosphoric acid
  • PpG
Chemical Formula: C10H15N5O11P2
Average Molecular Weight: 443.2005
Monoisotopic Molecular Weight: 443.024329371
InChI Key: QGWNDRXFNXRZMB-UUOKFMHZSA-N
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)/t3-,5-,6-,9-/m1/s1
CAS number: 146-91-8
IUPAC Name:[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name: GDP
SMILES:NC1=NC2=C(N=CN2[C@@H]2O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]2O)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
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Hypoxanthine
  • 6-oxopurine
  • Purine
  • Imidazopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Imidazole
  • Azole
  • Secondary alcohol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular Framework Aromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
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: Cytoplasm
Reactions:
Guanosine diphosphate + Reduced Thioredoxin > dGDP + Water + Oxidized Thioredoxin
Guanosine diphosphate + glutaredoxin > dGDP + glutaredoxin + Water
Adenosine triphosphate + Guanosine diphosphate <> ADP + Guanosine triphosphate
Adenosine triphosphate + Guanosine triphosphate + Water + Sulfate > Adenosine phosphosulfate + Guanosine diphosphate + Phosphate + Pyrophosphate
Adenosine triphosphate + Guanosine diphosphate > Adenosine monophosphate + Hydrogen ion + Guanosine 3',5'-bis(diphosphate)
P1,P4-Bis(5'-guanosyl) tetraphosphate + Water >2 Guanosine diphosphate +2 Hydrogen ion
Adenosine monophosphate + Guanosine triphosphate <> ADP + Guanosine diphosphate
Guanosine triphosphate + Water > Guanosine diphosphate + Hydrogen ion + Phosphate
Guanosine diphosphate + Hydrogen ion + D-Mannose 1-phosphate > Guanosine diphosphate mannose + Phosphate
Guanosine diphosphate mannose + Water > Guanosine diphosphate + Hydrogen ion + D-Mannose
Cytidine + Guanosine triphosphate > Cytidine monophosphate + Guanosine diphosphate + Hydrogen ion
Guanosine triphosphate + Uridine > Guanosine diphosphate + Hydrogen ion + Uridine 5'-monophosphate
Adenosine triphosphate + Guanosine monophosphate <> ADP + Guanosine diphosphate
Water + Guanosine 3',5'-bis(diphosphate) <> Guanosine diphosphate + Pyrophosphate
L-Aspartic acid + Guanosine triphosphate + Inosinic acid <> Adenylsuccinic acid + Guanosine diphosphate +2 Hydrogen ion + Phosphate
Guanosine triphosphate + Pyruvic acid <> Guanosine diphosphate + Phosphoenolpyruvic acid
RNA + Phosphate <> RNA + Guanosine diphosphate
Guanosine triphosphate + Cytidine <> Guanosine diphosphate + Cytidine monophosphate
Guanosine triphosphate + Uridine <> Guanosine diphosphate + Uridine 5'-monophosphate
Guanosine triphosphate + Inosinic acid + L-Aspartic acid <> Guanosine diphosphate + Phosphate + Adenylsuccinic acid
dGDP + Thioredoxin disulfide + Water <> Guanosine diphosphate + Thioredoxin
Adenosyl cobinamide + Guanosine triphosphate <> Adenosyl cobinamide phosphate + Guanosine diphosphate
L-Aspartic acid + Inosinic acid + Guanosine triphosphate > Hydrogen ion + adenylo-succinate + Phosphate + Guanosine diphosphate
GDP-&alpha;-D-glucose + Water > Hydrogen ion + b-D-Glucose + Guanosine diphosphate
Adenosine triphosphate + Guanosine diphosphate > Adenosine monophosphate + Guanosine 3',5'-bis(diphosphate)
Guanosine diphosphate + Water > Hydrogen ion + Guanosine monophosphate + Phosphate
Guanosine 3',5'-bis(diphosphate) + Water > Hydrogen ion + Pyrophosphate + Guanosine diphosphate
Guanosine diphosphate mannose + Water > Guanosine diphosphate + D-Mannose
Guanosine triphosphate + Water > Guanosine diphosphate + Inorganic phosphate
Adenosine triphosphate + Guanosine triphosphate + Adenosyl cobinamide <> Adenosyl cobinamide phosphate + ADP + Guanosine diphosphate
Succinyl-CoA + Phosphate + Guanosine diphosphate + Succinyl-CoA <> Succinic acid + Coenzyme A + Guanosine triphosphate
Guanosine triphosphate + Inosinic acid + L-Aspartic acid + L-Aspartic acid > Guanosine diphosphate + Phosphate + N(6)-(1,2-dicarboxyethyl)AMP
Inosinic acid + L-Aspartic acid + Guanosine triphosphate + L-Aspartic acid > Guanosine diphosphate + Phosphate +2 Hydrogen ion + N(6)-(1,2-dicarboxyethyl)AMP + Adenylsuccinic acid
Guanosine monophosphate + Adenosine triphosphate > Adenosine diphosphate + Guanosine diphosphate + ADP
Guanosine diphosphate + Adenosine triphosphate > Adenosine diphosphate + Guanosine triphosphate + ADP
Guanosine diphosphate + reduced thioredoxin > oxidized thioredoxin + Water + dGDP + dGDP
Guanosine diphosphate + a reduced NrdH glutaredoxin-like protein > Water + an oxidized NrdH glutaredoxin-like protein + dGDP + dGDP
More...

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:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Buchholz, A., Takors, R., Wandrey, C. (2001). "Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques." Anal Biochem 295:129-137. Pubmed: 11488613
  • Chantin C, Bonin B, Boulieu R, Bory C: Liquid-chromatographic study of purine metabolism abnormalities in purine nucleoside phosphorylase deficiency. Clin Chem. 1996 Feb;42(2):326-8. Pubmed: 8595732
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • 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
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
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
CHEBI ID17552
HMDB IDHMDB01201
Pubchem Compound ID8977
Kegg IDC00035
ChemSpider ID8630
WikipediaGDP
BioCyc IDGDP
EcoCyc IDGDP
Ligand ExpoGDP

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 RNA binding
Specific function:
Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction
Gene Name:
pnp
Locus Tag:
PA4740
Molecular weight:
75.4 kDa
Reactions
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.
General function:
Involved in bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity
Specific function:
Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
Gene Name:
apaH
Locus Tag:
PA0590
Molecular weight:
32 kDa
Reactions
P(1),P(4)-bis(5'-adenosyl) tetraphosphate + H(2)O = 2 ADP.
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 adenylosuccinate synthase activity
Specific function:
Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first commited step in the biosynthesis of AMP from IMP
Gene Name:
purA
Locus Tag:
PA4938
Molecular weight:
46.8 kDa
Reactions
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP.
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 nucleotide binding
Specific function:
ATP-dependent phosphorylation of adenosylcobinamide and adds GMP to adenosylcobinamide phosphate
Gene Name:
cobU
Locus Tag:
PA1279
Molecular weight:
36.5 kDa
Reactions
ATP or GTP + adenosylcobinamide = adenosylcobinamide phosphate + ADP or GDP.
GTP + adenosylcobinamide phosphate = diphosphate + adenosylcobinamide-GDP.
General function:
Involved in amino acid binding
Specific function:
In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes the formation of pppGpp which is then hydrolyzed to form ppGpp
Gene Name:
relA
Locus Tag:
PA0934
Molecular weight:
83.8 kDa
Reactions
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
General function:
Involved in catalytic activity
Specific function:
In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes both the synthesis and degradation of ppGpp. The second messengers ppGpp and c-di-GMP together control biofilm formation in response to translational stress; ppGpp represses biofilm formation while c- di-GMP induces it
Gene Name:
spoT
Locus Tag:
PA5338
Molecular weight:
78.9 kDa
Reactions
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
Guanosine 3',5'-bis(diphosphate) + H(2)O = guanosine 5'-diphosphate + diphosphate.
General function:
Involved in catalytic activity
Specific function:
ATP + sulfate = diphosphate + adenylyl sulfate
Gene Name:
cysD
Locus Tag:
PA4443
Molecular weight:
35.5 kDa
Reactions
ATP + sulfate = diphosphate + adenylyl sulfate.
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 GTPase activity
Specific function:
May be the GTPase, regulating ATP sulfurylase activity
Gene Name:
cysN
Locus Tag:
PA4442
Molecular weight:
69.3 kDa
Reactions
ATP + sulfate = diphosphate + adenylyl sulfate.
General function:
Involved in nucleotidyltransferase activity
Specific function:
Involved in the biosynthesis of the capsular polysaccharide colanic acid
Gene Name:
manC
Locus Tag:
PA3551
Molecular weight:
53.1 kDa
Reactions
GTP + alpha-D-mannose 1-phosphate = diphosphate + GDP-mannose.
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

Transporters

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.