You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-31 18:49:20 UTC
HMDB IDHMDB0001201
Secondary Accession Numbers
  • HMDB01201
Metabolite Identification
Common NameGuanosine diphosphate
DescriptionGuanosine 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
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, guanosineMeSH
Diphosphate, guanosine 5'-trihydrogenMeSH
Guanosine 5' diphosphateMeSH
Guanosine 5' trihydrogen diphosphateMeSH
5'-Trihydrogen diphosphate, guanosineMeSH
Diphosphate, guanosineMeSH
Guanosine 5'-trihydrogen diphosphateMeSH
Chemical FormulaC10H15N5O11P2
Average Molecular Weight443.2005
Monoisotopic Molecular Weight443.024329371
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 NameGDP
CAS Registry Number146-91-8
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
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
DescriptionThis compound belongs to the class of chemical entities known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
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
  • Pyrimidone
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Pyrimidine
  • Alkyl phosphate
  • N-substituted imidazole
  • Primary aromatic amine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Monosaccharide
  • Vinylogous amide
  • Heteroaromatic compound
  • Imidazole
  • Oxolane
  • Azole
  • Secondary alcohol
  • 1,2-diol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Alcohol
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organic nitrogen compound
  • Amine
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

  Health condition:

    Nervous system disorders:

Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

  Cell and elements:

Source:

Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Role

Industrial application:

  Pharmaceutical industry:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility4.44 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity86.37 m³·mol⁻¹ChemAxon
Polarizability35.28 ųChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
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
  • Extracellular
  • Mitochondria
  • Nucleus
  • Golgi apparatus
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
2-ketoglutarate dehydrogenase complex deficiencyPw000525Pw000525 greyscalePw000525 simpleNot Available
AICA-RibosiduriaPw000082Pw000082 greyscalePw000082 simpleNot Available
Acrivastine H1-Antihistamine ActionPw060826Pw060826 greyscalePw060826 simpleNot Available
Activation of PKC through G protein coupled receptorPw000726Pw000726 greyscalePw000726 simpleNot Available
Adenine phosphoribosyltransferase deficiency (APRT)Pw000511Pw000511 greyscalePw000511 simpleNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified15.0 +/- 2.0 uMAdult (>18 years old)MaleNormal
    • Geigy Scientific ...
details
BloodDetected and Quantified18.0 +/- 8.0 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Cerebrospinal Fluid (CSF)Detected and Quantified1.86 +/- 0.027 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified2.11 +/- 1.93 uMAdult (>18 years old)BothRachialgia details
Cerebrospinal Fluid (CSF)Detected and Quantified4.05 +/- 0.03 uMAdult (>18 years old)BothSubarachnoid hemorrhage details
Cerebrospinal Fluid (CSF)Detected and Quantified0.99 +/- 1.32 uMAdult (>18 years old)BothEpilepsy details
Cerebrospinal Fluid (CSF)Detected and Quantified2.55 +/- 1.62 uMAdult (>18 years old)Both
Stroke
details
Cerebrospinal Fluid (CSF)Detected and Quantified2.59 +/- 1.77 uMAdult (>18 years old)BothNeuroinfection details
Associated Disorders and Diseases
Disease References
Subarachnoid hemorrhage
  1. Czarnecka J, Cieslak M, Michal K: Application of solid phase extraction and high-performance liquid chromatography to qualitative and quantitative analysis of nucleotides and nucleosides in human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Aug 5;822(1-2):85-90. [PubMed:15993662 ]
Epilepsy
  1. Czarnecka J, Cieslak M, Michal K: Application of solid phase extraction and high-performance liquid chromatography to qualitative and quantitative analysis of nucleotides and nucleosides in human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Aug 5;822(1-2):85-90. [PubMed:15993662 ]
Neuroinfection
  1. Czarnecka J, Cieslak M, Michal K: Application of solid phase extraction and high-performance liquid chromatography to qualitative and quantitative analysis of nucleotides and nucleosides in human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Aug 5;822(1-2):85-90. [PubMed:15993662 ]
Rachialgia
  1. Czarnecka J, Cieslak M, Michal K: Application of solid phase extraction and high-performance liquid chromatography to qualitative and quantitative analysis of nucleotides and nucleosides in human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Aug 5;822(1-2):85-90. [PubMed:15993662 ]
Stroke
  1. Czarnecka J, Cieslak M, Michal K: Application of solid phase extraction and high-performance liquid chromatography to qualitative and quantitative analysis of nucleotides and nucleosides in human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Aug 5;822(1-2):85-90. [PubMed:15993662 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022487
KNApSAcK IDNot Available
Chemspider ID8630
KEGG Compound IDC00035
BioCyc IDGDP
BiGG ID33599
Wikipedia LinkGuanosine diphosphate
METLIN ID6077
PubChem Compound8977
PDB IDGDP
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 References
  1. 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 ]

Only showing the first 10 proteins. There are 230 proteins in total.

Enzymes

General function:
Involved in hydrolase activity
Specific function:
In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. Hydrolyzes ATP and ADP equally well.
Gene Name:
ENTPD1
Uniprot ID:
P49961
Molecular weight:
58706.0
Reactions
Guanosine diphosphate + Water → Guanosine monophosphate + Phosphoric aciddetails
Guanosine triphosphate + Water → Guanosine diphosphate + Phosphoric aciddetails
General function:
Involved in calcium ion binding
Specific function:
Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP. Involved in proteoglycan synthesis.
Gene Name:
CANT1
Uniprot ID:
Q8WVQ1
Molecular weight:
44839.24
Reactions
Guanosine diphosphate + Water → Guanosine monophosphate + Phosphoric aciddetails
General function:
Involved in hydrolase activity
Specific function:
Has a threefold preference for the hydrolysis of ATP over ADP.
Gene Name:
ENTPD3
Uniprot ID:
O75355
Molecular weight:
59104.76
Reactions
Guanosine diphosphate + Water → Guanosine monophosphate + Phosphoric aciddetails
Guanosine triphosphate + Water → Guanosine diphosphate + Phosphoric aciddetails
General function:
Involved in ATP binding
Specific function:
Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4-thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)-benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5-methylcytidine, and N(4)-anisoylcytidine.
Gene Name:
UCK1
Uniprot ID:
Q9HA47
Molecular weight:
22760.43
Reactions
Guanosine triphosphate + Cytidine → Guanosine diphosphate + Cytidine monophosphatedetails
Guanosine triphosphate + Uridine → Guanosine diphosphate + Uridine 5'-monophosphatedetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP (By similarity).
Gene Name:
NME4
Uniprot ID:
O00746
Molecular weight:
20658.45
Reactions
Adenosine triphosphate + Guanosine diphosphate → ADP + Guanosine triphosphatedetails
General function:
Involved in oxidation reduction
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:
RRM1
Uniprot ID:
P23921
Molecular weight:
90069.375
Reactions
dGDP + Thioredoxin disulfide + Water → Guanosine diphosphate + Thioredoxindetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Possesses nucleoside-diphosphate kinase, serine/threonine-specific protein kinase, geranyl and farnesyl pyrophosphate kinase, histidine protein kinase and 3'-5' exonuclease activities. Involved in cell proliferation, differentiation and development, signal transduction, G protein-coupled receptor endocytosis, and gene expression. Required for neural development including neural patterning and cell fate determination.
Gene Name:
NME1
Uniprot ID:
P15531
Molecular weight:
17148.635
Reactions
Adenosine triphosphate + Guanosine diphosphate → ADP + Guanosine triphosphatedetails
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:
NME7
Uniprot ID:
Q9Y5B8
Molecular weight:
42491.365
Reactions
Adenosine triphosphate + Guanosine diphosphate → ADP + Guanosine triphosphatedetails
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Inhibits Wnt signaling.
Gene Name:
RRM2
Uniprot ID:
P31350
Molecular weight:
44877.25
Reactions
dGDP + Thioredoxin disulfide + Water → Guanosine diphosphate + Thioredoxindetails
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. Negatively regulates Rho activity by interacting with AKAP13/LBC. Acts as a transcriptional activator of the MYC gene; binds DNA non-specifically (PubMed:8392752). Exhibits histidine protein kinase activity.
Gene Name:
NME2
Uniprot ID:
P22392
Molecular weight:
30136.92
Reactions
Adenosine triphosphate + Guanosine diphosphate → ADP + Guanosine triphosphatedetails

Only showing the first 10 proteins. There are 230 proteins in total.