Human Metabolome Database: Showing metabocard for Guanosine diphosphate (HMDB0001201)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (230) Show 230 proteins XML

enzymes (230) Show 230 proteins

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2020-05-07 17:14:32 UTC

HMDB ID

HMDB0001201

Secondary Accession Numbers

HMDB01201

Metabolite Identification

Common Name

Guanosine diphosphate

Description

Guanosine diphosphate, also known as 5'-GDP or 5'-diphosphate, guanosine, 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 a moderately basic compound (based on its pKa). Guanosine diphosphate exists in all living species, ranging from bacteria to humans. In humans, guanosine diphosphate is involved in intracellular signalling through adenosine receptor A2B and adenosine. Outside of the human body, Guanosine diphosphate has been detected, but not quantified in, several different foods, such as devilfish, java plums, green beans, almonds, and orange mints. This could make guanosine diphosphate a potential biomarker for the consumption of these foods. A purine ribonucleoside 5'-diphosphate resulting from the formal condensation of the hydroxy group at the 5' position of guanosine with pyrophosphoric acid.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Guanosine 5'-diphosphate	ChEBI
Guanosine 5'-diphosphoric acid	Generator
Guanosine diphosphoric acid	Generator
5'-GDP	HMDB
GDP	HMDB
Guanosine 5'-(trihydrogen pyrophosphate)	HMDB
Guanosine 5'-pyrophosphate	HMDB
Guanosine mono(trihydrogen diphosphate)	HMDB
Guanosine pyrophosphate	HMDB
Guanosine-5'-diphosphate	HMDB
Guanosine-diphosphate	HMDB
PpG	HMDB
5'-Diphosphate, guanosine	HMDB
Diphosphate, guanosine 5'-trihydrogen	HMDB
Guanosine 5' diphosphate	HMDB
Guanosine 5' trihydrogen diphosphate	HMDB
5'-Trihydrogen diphosphate, guanosine	HMDB
Diphosphate, guanosine	HMDB
Guanosine 5'-trihydrogen diphosphate	HMDB

Chemical Formula

C₁₀H₁₅N₅O₁₁P₂

Average Molecular Weight

443.2005

Monoisotopic Molecular Weight

443.024329371

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 Number

146-91-8

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 Key

QGWNDRXFNXRZMB-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.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine 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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine ribonucleoside 5'-diphosphate (CHEBI:17552 )
guanosine 5'-phosphate (CHEBI:17552 )
Ribonucleotides (C00035 )

Ontology

Physiological effect

Health effect:

Health condition:

Nervous system disorders:

Stroke

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Biofluid and excreta:

Subcellular:

Cell and elements:

Extracellular

Process

Naturally occurring process:

Biological process:

Biochemical pathway:

Role

Industrial application:

Pharmaceutical industry:

Pharmaceutical

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	4.44 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-3.7	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	1.71	ChemAxon
pKa (Strongest Basic)	2.55	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	248.28 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	85.93 m³·mol⁻¹	ChemAxon
Polarizability	34.74 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-5930200000-bdc0893316c12636a495	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0229-6393250000-a57b7f18975223fa888c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0udl-0900600000-5c7173a5771dfefadc5e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0udi-0900000000-d38af29994fa5108c331	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0udi-0900000000-3072d857dcc8a1b2cbaa	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-0kdi-5901100000-24a5c807e53370f01d0c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-0udi-0900000000-6399eaf97235815c4cb7	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0911300000-fcd49d8a5e9d3dc3f933	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-ded96f0f499982ac1ab0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0900000000-ac93e95f54842f42e273	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6x-0900800000-1ed1199fdace4d1b4d80	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zir-3900000000-b9aeef613c34fe99a48c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-f630c9237e72a76d3d63	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Mitochondria
Nucleus
Golgi apparatus

Biospecimen Locations

Blood
Cerebrospinal Fluid (CSF)

Tissue Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Citric Acid Cycle
Gluconeogenesis
Purine Metabolism
Aspartate Metabolism
Canavan Disease		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	15.0 +/- 2.0 uM	Adult (>18 years old)	Male	Normal	Geigy Scientific ...	details
Blood	Detected and Quantified	18.0 +/- 8.0 uM	Adult (>18 years old)	Both	Normal	Geigy Scientific ...	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	1.86 +/- 0.027 uM	Adult (>18 years old)	Both	Normal	15993662	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Cerebrospinal Fluid (CSF)	Detected and Quantified	2.11 +/- 1.93 uM	Adult (>18 years old)	Both	Rachialgia	15993662	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	4.05 +/- 0.03 uM	Adult (>18 years old)	Both	Subarachnoid hemorrhage	15993662	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	0.99 +/- 1.32 uM	Adult (>18 years old)	Both	Epilepsy	15993662	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	2.55 +/- 1.62 uM	Adult (>18 years old)	Both	Stroke	15993662	details
Cerebrospinal Fluid (CSF)	Detected and Quantified	2.59 +/- 1.77 uM	Adult (>18 years old)	Both	Neuroinfection	15993662	details

Associated Disorders and Diseases

Disease References

Rachialgia
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 ]
Subarachnoid hemorrhage
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
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
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
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

105800 (Subarachnoid hemorrhage)
601367 (Stroke)

External Links

DrugBank ID

DB04315

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030875

KNApSAcK ID

Not Available

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

Guanosine diphosphate

METLIN ID

6077

PubChem Compound

8977

PDB ID

Not Available

ChEBI ID

17552

Food Biomarker Ontology

Not Available

VMH ID

GDP

References

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

General References

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.

Show all enzymes and transporters

Enzymes

Enzyme Details

1. Ectonucleoside triphosphate diphosphohydrolase 1

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 + Phosphate	details
Guanosine triphosphate + Water → Guanosine diphosphate + Phosphate	details

Enzyme Details

2. Soluble calcium-activated nucleotidase 1

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 + Phosphate	details

Enzyme Details

3. Ectonucleoside triphosphate diphosphohydrolase 3

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 + Phosphate	details
Guanosine triphosphate + Water → Guanosine diphosphate + Phosphate	details

Enzyme Details

4. Uridine-cytidine kinase 1

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 monophosphate	details
Guanosine triphosphate + Uridine → Guanosine diphosphate + Uridine 5'-monophosphate	details

Enzyme Details

5. Nucleoside diphosphate kinase, mitochondrial

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 triphosphate	details

Enzyme Details

6. Ribonucleoside-diphosphate reductase large subunit

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 + Thioredoxin	details

Enzyme Details

7. Nucleoside diphosphate kinase A

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 triphosphate	details

Enzyme Details

8. Nucleoside diphosphate kinase 7

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 triphosphate	details

Enzyme Details

9. Ribonucleoside-diphosphate reductase subunit M2

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 + Thioredoxin	details

Enzyme Details

10. Nucleoside diphosphate kinase B

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 triphosphate	details

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

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Showing metabocard for Guanosine diphosphate (HMDB0001201)

Structure for HMDB0001201 (Guanosine diphosphate)

Enzymes

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