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Showing metabocard for Guanosine diphosphate (BMDB0001201)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (13) Show 13 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:42:31 UTC
Update Date2020-05-21 16:29:08 UTC
BMDB IDBMDB0001201
Secondary Accession Numbers
  • BMDB01201
Metabolite Identification
Common NameGuanosine diphosphate
DescriptionGuanosine diphosphate, also known as Guanosine diphosphate or GDP, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Guanosine diphosphate is possibly soluble (in water) and a moderately basic compound (based on its pKa). Guanosine diphosphate exists in all living species, ranging from bacteria to humans. In cattle, guanosine diphosphate is involved in a couple of metabolic pathways, which include the intracellular signalling through adenosine receptor A2A and adenosine pathway and the intracellular signalling through adenosine receptor A2B and adenosine pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
Guanosine 5'-diphosphateChEBI
Guanosine 5'-diphosphoric acidGenerator
Guanosine diphosphoric acidGenerator
5'-GDPHMDB
GDPHMDB
Guanosine 5'-(trihydrogen pyrophosphate)HMDB
Guanosine 5'-pyrophosphateHMDB
Guanosine mono(trihydrogen diphosphate)HMDB
Guanosine pyrophosphateHMDB
Guanosine-5'-diphosphateHMDB
Guanosine-diphosphateHMDB
PpGHMDB
5'-Diphosphate, guanosineHMDB
Diphosphate, guanosine 5'-trihydrogenHMDB
Guanosine 5' diphosphateHMDB
Guanosine 5' trihydrogen diphosphateHMDB
5'-Trihydrogen diphosphate, guanosineHMDB
Diphosphate, guanosineHMDB
Guanosine 5'-trihydrogen diphosphateHMDB
Chemical FormulaC10H15N5O11P2
Average Molecular Weight443.2005
Monoisotopic Molecular Weight443.024329371
IUPAC Name[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry Number146-91-8
SMILES
NC1=NC(=O)C2=C(N1)N(C=N2)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier
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
InChI KeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Purine ribonucleoside monophosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-oxopurine
  • Hypoxanthine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Secondary alcohol
  • 1,2-diol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organooxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Alcohol
  • Amine
  • Organic oxygen compound
  • Primary amine
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Golgi
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.5ALOGPS
logP-3.7ChemAxon
logS-2ALOGPS
pKa (Strongest Acidic)1.71ChemAxon
pKa (Strongest Basic)2.55ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area248.28 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity85.93 m³·mol⁻¹ChemAxon
Polarizability34.74 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-5930200000-bdc0893316c12636a495View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0229-6393250000-a57b7f18975223fa888cView in MoNA
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
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-0kdi-5901100000-24a5c807e53370f01d0cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-0udi-0900000000-6399eaf97235815c4cb7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0911300000-fcd49d8a5e9d3dc3f933View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-ded96f0f499982ac1ab0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-ac93e95f54842f42e273View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6x-0900800000-1ed1199fdace4d1b4d80View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0zir-3900000000-b9aeef613c34fe99a48cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-f630c9237e72a76d3d63View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Golgi
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001201
DrugBank IDDB04315
Phenol Explorer Compound IDNot Available
FooDB IDFDB030875
KNApSAcK IDNot Available
Chemspider ID8630
KEGG Compound IDC00035
BioCyc IDGDP
BiGG ID33599
Wikipedia LinkGuanosine diphosphate
METLIN ID6077
PubChem Compound8977
PDB IDNot Available
ChEBI ID17552
References
Synthesis ReferenceEdlin, 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
General ReferencesNot Available

Enzymes

Enzyme Details
1. Ectonucleoside triphosphate diphosphohydrolase 8
General function:
Not Available
Specific function:
Canalicular ectonucleoside NTPDase responsible for the main hepatic NTPDase activity. Ectonucleoside NTPDases catalyze the hydrolysis of gamma- and beta-phosphate residues of nucleotides, playing a central role in concentration of extracellular nucleotides. Has activity toward ATP, ADP, UTP and UDP, but not toward AMP (By similarity).
Gene Name:
ENTPD8
Uniprot ID:
A0JND9
Molecular weight:
53240.0
Reactions
Guanosine triphosphate + Water → Guanosine diphosphate + Hydrogen phosphatedetails
Enzyme Details
2. Nucleoside diphosphate kinase 7
General function:
Nucleotide transport and metabolism
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 (By similarity).
Gene Name:
NME7
Uniprot ID:
Q5E9Y9
Molecular weight:
42599.0
Reactions
Adenosine triphosphate + Guanosine diphosphate → ADP + Guanosine triphosphatedetails
Enzyme Details
3. Adenylosuccinate synthetase isozyme 1
General function:
Nucleotide transport and metabolism
Specific function:
Component of the purine nucleotide cycle (PNC), which interconverts IMP and AMP to regulate the nucleotide levels in various tissues, and which contributes to glycolysis and ammoniagenesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP.
Gene Name:
ADSS1
Uniprot ID:
A5PJR4
Molecular weight:
50134.0
Reactions
Guanosine triphosphate + Inosinic acid + L-Aspartic acid → Guanosine diphosphate + Hydrogen phosphate + Adenylsuccinic aciddetails
Enzyme Details
4. Adenylosuccinate synthetase isozyme 2
General function:
Nucleotide transport and metabolism
Specific function:
Plays an important role in the de novo pathway and in the salvage pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP.
Gene Name:
ADSS2
Uniprot ID:
A7MBG0
Molecular weight:
50156.0
Reactions
Guanosine triphosphate + Inosinic acid + L-Aspartic acid → Guanosine diphosphate + Hydrogen phosphate + Adenylsuccinic aciddetails
Enzyme Details
5. Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
General function:
Energy production and conversion
Specific function:
Regulates cataplerosis and anaplerosis, the processes that control the levels of metabolic intermediates in the citric acid cycle. At low glucose levels, it catalyzes the cataplerotic conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP), the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle. At high glucose levels, it catalyzes the anaplerotic conversion of phosphoenolpyruvate to oxaloacetate.
Gene Name:
PCK1
Uniprot ID:
Q8HYZ4
Molecular weight:
69353.0
Reactions
Guanosine triphosphate + Oxalacetic acid → Guanosine diphosphate + Phosphoenolpyruvic acid + Carbon dioxidedetails
Enzyme Details
6. Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
General function:
Energy production and conversion
Specific function:
Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and specificity for either ATP or GTP is provided by different beta subunits.
Gene Name:
SUCLG1
Uniprot ID:
Q58DR8
Molecular weight:
36167.0
Reactions
Succinyl-CoA + Hydrogen phosphate + Guanosine diphosphate → Succinic acid + Coenzyme A + Guanosine triphosphatedetails
Enzyme Details
7. Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
General function:
Energy production and conversion
Specific function:
GTP-specific succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit.
Gene Name:
SUCLG2
Uniprot ID:
Q3MHX5
Molecular weight:
46691.0
Reactions
Succinyl-CoA + Hydrogen phosphate + Guanosine diphosphate → Succinic acid + Coenzyme A + Guanosine triphosphatedetails
Enzyme Details
8. Guanylate kinase
General function:
Nucleotide transport and metabolism
Specific function:
Catalyzes the phosphorylation of GMP to GDP. Essential enzyme for recycling GMP and indirectly, cyclic GMP (cGMP) (PubMed:8243671, PubMed:29515371, PubMed:7911663). Involved in the cGMP metabolism in photoreceptors (PubMed:29515371, PubMed:8243671).
Gene Name:
GUK1
Uniprot ID:
P46195
Molecular weight:
21910.0
Reactions
Adenosine triphosphate + Guanosine monophosphate → ADP + Guanosine diphosphatedetails
Enzyme Details
9. Ectonucleoside triphosphate diphosphohydrolase 5
General function:
Not Available
Specific function:
Uridine diphosphatase (UDPase) that promotes protein N-glycosylation and ATP level regulation. UDP hydrolysis promotes protein N-glycosylation and folding in the endoplasmic reticulum, as well as elevated ATP consumption in the cytosol via an ATP hydrolysis cycle. Together with CMPK1 and AK1, constitutes an ATP hydrolysis cycle that converts ATP to AMP and results in a compensatory increase in aerobic glycolysis. The nucleotide hydrolyzing preference is GDP > IDP > UDP, but not any other nucleoside di-, mono- or triphosphates, nor thiamine pyrophosphate. Plays a key role in the AKT1-PTEN signaling pathway by promoting glycolysis in proliferating cells in response to phosphoinositide 3-kinase (PI3K) signaling (By similarity).
Gene Name:
ENTPD5
Uniprot ID:
E1BPW0
Molecular weight:
47888.0
Reactions
Guanosine diphosphate + Water → Guanosine monophosphate + Hydrogen phosphatedetails
Guanosine triphosphate + Water → Guanosine diphosphate + Hydrogen phosphatedetails
Enzyme Details
10. Rap guanine nucleotide exchange factor 2
General function:
Not Available
Specific function:
Functions as a guanine nucleotide exchange factor (GEF), which activates Rap and Ras family of small GTPases by exchanging bound GDP for free GTP in a cAMP-dependent manner. Serves as a link between cell surface receptors and Rap/Ras GTPases in intracellular signaling cascades. Acts also as an effector for Rap1 by direct association with Rap1-GTP thereby leading to the amplification of Rap1-mediated signaling. Shows weak activity on HRAS. It is controversial whether RAPGEF2 binds cAMP and cGMP or not. Its binding to ligand-activated beta-1 adrenergic receptor ADRB1 leads to the Ras activation through the G(s)-alpha signaling pathway. Involved in the cAMP-induced Ras and Erk1/2 signaling pathway that leads to sustained inhibition of long term melanogenesis by reducing dendrite extension and melanin synthesis. Provides also inhibitory signals for cell proliferation of melanoma cells and promotes their apoptosis in a cAMP-independent nanner. Regulates cAMP-induced neuritogenesis by mediating the Rap1/B-Raf/ERK signaling through a pathway that is independent on both PKA and RAPGEF3/RAPGEF4. Involved in neuron migration and in the formation of the major forebrain fiber connections forming the corpus callosum, the anterior commissure and the hippocampal commissure during brain development. Involved in neuronal growth factor (NGF)-induced sustained activation of Rap1 at late endosomes and in brain-derived neurotrophic factor (BDNF)-induced axon outgrowth of hippocampal neurons. Plays a role in the regulation of embryonic blood vessel formation and in the establishment of basal junction integrity and endothelial barrier function. May be involved in the regulation of the vascular endothelial growth factor receptor KDR and cadherin CDH5 expression at allantois endothelial cell-cell junctions (By similarity). Binds to cAMP.
Gene Name:
RAPGEF2
Uniprot ID:
F1MSG6
Molecular weight:
165144.0
Reactions
Cyclic AMP + Rap guanine nucleotide exchange factor 3 + Guanosine triphosphate + Ras-related protein Rap-1A → Guanosine diphosphate + Ras-related protein Rap-1Adetails
GTPase HRas with GDP + Guanosine triphosphate → GTPase HRas with GTP + Guanosine diphosphatedetails
Enzyme Details
11. Rho guanine nucleotide exchange factor 9
General function:
Not Available
Specific function:
Acts as guanine nucleotide exchange factor (GEF) for CDC42. Promotes formation of GPHN clusters (By similarity).
Gene Name:
ARHGEF9
Uniprot ID:
Q58DL7
Molecular weight:
65980.0
Reactions
Cell division control protein 42 homolog with GDP + Guanosine triphosphate → Cell division control protein 42 homolog with GTP + Guanosine diphosphatedetails
Enzyme Details
12. Ribonucleotide reductase regulatory subunit M2
General function:
Not Available
Specific function:
Not Available
Gene Name:
RRM2
Uniprot ID:
E1BI58
Molecular weight:
44821.0
Reactions
dGDP + Thioredoxin Disulfide + Water → Guanosine diphosphate + Thioredoxindetails
Enzyme Details
13. Ribonucleoside-diphosphate reductase
General function:
Not Available
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:
RRM1
Uniprot ID:
F1MSF1
Molecular weight:
89991.0
Reactions
dGDP + Thioredoxin Disulfide + Water → Guanosine diphosphate + Thioredoxindetails