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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-09-21 17:57:24 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 chemical entities 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.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
Direct ParentPurine 2'-deoxyribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine 2'-deoxyribonucleoside diphosphate
  • 6-oxopurine
  • Hypoxanthine
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Alkyl phosphate
  • Heteroaromatic compound
  • Vinylogous amide
  • Azole
  • Oxolane
  • Imidazole
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Amine
  • Primary amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
Biofunction
  • DNA component
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity84.86 m3·mol-1ChemAxon
Polarizability34.99 Å3ChemAxon
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-MSNot Available
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, 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
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biofluid LocationsNot Available
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
AICA-RibosiduriaPw000082Pw000082 greyscalePw000082 simpleNot Available
Adenine phosphoribosyltransferase deficiency (APRT)Pw000511Pw000511 greyscalePw000511 simpleNot Available
Adenosine Deaminase DeficiencyPw000075Pw000075 greyscalePw000075 simpleNot Available
Adenylosuccinate Lyase DeficiencyPw000076Pw000076 greyscalePw000076 simpleNot Available
Azathioprine PathwayPw000266Pw000266 greyscalePw000266 simpleNot Available
Displaying entries 1 - 5 of 17 in total
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022338
KNApSAcK IDNot Available
Chemspider ID388359
KEGG Compound IDC00361
BioCyc IDDGDP
BiGG ID34741
Wikipedia LinkNot Available
NuGOwiki LinkHMDB0000960
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 ]

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
General function:
Involved in magnesium ion binding
Specific function:
Plays a key role in glycolysis (By similarity).
Gene Name:
PKLR
Uniprot ID:
P30613
Molecular weight:
61829.575
Reactions
dGTP + Pyruvic acid → dGDP + Phosphoenolpyruvic aciddetails
General function:
Involved in guanylate kinase activity
Specific function:
Essential for recycling GMP and indirectly, cGMP.
Gene Name:
GUK1
Uniprot ID:
Q16774
Molecular weight:
21725.41
Reactions
Adenosine triphosphate + 2'-Deoxyguanosine 5'-monophosphate → ADP + dGDPdetails
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:
UCK2
Uniprot ID:
Q9BZX2
Molecular weight:
29298.92
Reactions
dGTP + Uridine → dGDP + Uridine 5'-monophosphatedetails
dGTP + Cytidine → dGDP + Cytidine monophosphatedetails
General function:
Involved in oxidoreductase activity
Specific function:
Plays a pivotal role in cell survival by repairing damaged DNA in a p53/TP53-dependent manner. Supplies deoxyribonucleotides for DNA repair in cells arrested at G1 or G2. Contains an iron-tyrosyl free radical center required for catalysis. Forms an active ribonucleotide reductase (RNR) complex with RRM1 which is expressed both in resting and proliferating cells in response to DNA damage.
Gene Name:
RRM2B
Uniprot ID:
Q7LG56
Molecular weight:
48786.6
Reactions
dGDP + Thioredoxin disulfide + Water → Guanosine diphosphate + Thioredoxindetails
General function:
Involved in ATP binding
Specific function:
May contribute to UTP accumulation needed for blast transformation and proliferation.
Gene Name:
UCKL1
Uniprot ID:
Q9NWZ5
Molecular weight:
59465.77
Reactions
dGTP + Uridine → dGDP + Uridine 5'-monophosphatedetails
dGTP + Cytidine → dGDP + Cytidine monophosphatedetails
General function:
Not Available
Specific function:
Does not seem to have NDK kinase activity. Confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. May play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species (By similarity).
Gene Name:
NME5
Uniprot ID:
P56597
Molecular weight:
Not Available
Reactions
Adenosine triphosphate + dGDP → ADP + dGTPdetails