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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-20 20:29:41 UTC
HMDB IDHMDB0000960
Secondary Accession Numbers
  • HMDB00960
Metabolite Identification
Common NamedGDP
DescriptiondGDP is a derivative of the common nucleic acid GTP, or guanosine triphosphate, in which the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose has been removed (hence the deoxy- part of the name). Additionally, the diphosphate of the name indicates that one of the phosphoryl groups of GTP has been removed, most likely by hydrolysis (Wikipedia).
Structure
Thumb
Synonyms
ValueSource
2'-Deoxyguanosine 5'-diphosphateChEBI
Deoxyguanosine diphosphateChEBI
2'-Deoxyguanosine 5'-diphosphoric acidGenerator
Deoxyguanosine diphosphoric acidGenerator
2'-Deoxy-GDPHMDB
2'-Deoxyguanosine-5'-diphosphateHMDB
5'-dGDPHMDB
Deoxyguanosine 5'-diphosphateHMDB
Deoxyguanosine-diphosphateHMDB
Chemical FormulaC10H15N5O10P2
Average Molecular Weight427.2011
Monoisotopic Molecular Weight427.029414749
IUPAC Name[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional NamedGDP
CAS Registry Number3493-09-2
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
InChI Identifier
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
InChI KeyCIKGWCTVFSRMJU-KVQBGUIXSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine deoxyribonucleotides
Direct ParentPurine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside diphosphate
  • 6-oxopurine
  • Hypoxanthine
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Pyrimidine
  • Heteroaromatic compound
  • Azole
  • Imidazole
  • Vinylogous amide
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Primary amine
  • Organic oxide
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility5.5 mg/mLNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility3.6 g/LALOGPS
logP-1.4ALOGPS
logP-2.6ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)1.97ChemAxon
pKa (Strongest Basic)1.36ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area228.05 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.86 m³·mol⁻¹ChemAxon
Polarizability34.99 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, Positivesplash10-056v-8931100000-80ef9c9f635e7c791ca3View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-006w-9273200000-8578b4069f91a1e37a93View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-004i-9600800000-36eca5667f3968858676View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-0udi-2910000000-7d78949fd021bc9a3e84View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0901100000-8f9213d3d0d12989aa4eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0900000000-fe32d673485e026f7ffdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udi-0900000000-f9d9c2d10a52b1295c20View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0500900000-f643b08ebfbee486ac88View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-4900000000-614b7240ac447b1cf302View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-ebc82fc4fdc1243cf001View in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022338
KNApSAcK IDC00019355
Chemspider ID388359
KEGG Compound IDC00361
BioCyc IDDGDP
BiGG ID34741
Wikipedia LinkDeoxyguanosine_diphosphate
METLIN ID5906
PubChem Compound439220
PDB IDDGI
ChEBI ID28862
References
Synthesis ReferenceKlenow, Hans; Lichtler, Eleanor; Andersen, Bjorn. Adenine deoxyriboside polyphosphates. Acta Chemica Scandinavica (1956), 10 159-60
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Brady WA, Kokoris MS, Fitzgibbon M, Black ME: Cloning, characterization, and modeling of mouse and human guanylate kinases. J Biol Chem. 1996 Jul 12;271(28):16734-40. [PubMed:8663313 ]
  2. Nomanbhoy TK, Leonard DA, Manor D, Cerione RA: Investigation of the GTP-binding/GTPase cycle of Cdc42Hs using extrinsic reporter group fluorescence. Biochemistry. 1996 Apr 9;35(14):4602-8. [PubMed:8605211 ]
  3. Rothwell PS: The new MFGDP (UK) examination (formerly, the DGDP [UK]) Br Dent J. 1999 Oct 9;187(7):354-6. [PubMed:10581811 ]
  4. Bialkowski K, Kasprzak KS: Inhibition of 8-oxo-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase (8-oxo-dGTPase) activity of the antimutagenic human MTH1 protein by nucleoside 5'-diphosphates. Free Radic Biol Med. 2003 Sep 15;35(6):595-602. [PubMed:12957652 ]
  5. Kumar V, Spangenberg O, Konrad M: Cloning of the guanylate kinase homologues AGK-1 and AGK-2 from Arabidopsis thaliana and characterization of AGK-1. Eur J Biochem. 2000 Jan;267(2):606-15. [PubMed:10632732 ]

Only showing the first 10 proteins. There are 16 proteins in total.

Enzymes

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
dGTP + Uridine → dGDP + Uridine 5'-monophosphatedetails
dGTP + Cytidine → dGDP + Cytidine 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 + dGDP → ADP + dGTPdetails
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 + dGDP → ADP + dGTPdetails
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 + dGDP → ADP + dGTPdetails
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 + dGDP → ADP + dGTPdetails
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. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.
Gene Name:
NME3
Uniprot ID:
Q13232
Molecular weight:
19014.85
Reactions
Adenosine triphosphate + dGDP → ADP + dGTPdetails
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. Inhibitor of p53-induced apoptosis.
Gene Name:
NME6
Uniprot ID:
O75414
Molecular weight:
22002.965
Reactions
Adenosine triphosphate + dGDP → ADP + dGTPdetails
General function:
Involved in magnesium ion binding
Specific function:
Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.
Gene Name:
PKM
Uniprot ID:
P14618
Molecular weight:
65930.14
Reactions
dGTP + Pyruvic acid → dGDP + Phosphoenolpyruvic aciddetails

Only showing the first 10 proteins. There are 16 proteins in total.