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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-10-30 10:32:48 UTC
Update Date2022-03-07 03:17:34 UTC
HMDB IDHMDB0059648
Secondary Accession Numbers
  • HMDB59648
Metabolite Identification
Common Name8-oxo-dGDP
Description8-oxo-dGDP 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. 8-oxo-dGDP is a very strong basic compound (based on its pKa). In humans, 8-oxo-dGDP is involved in the metabolic disorder called the purine nucleoside phosphorylase deficiency pathway. 8-oxo-dgdp is part of the Purine metabolism pathway.
Structure
Data?1563865960
Synonyms
ValueSource
2'-Deoxy-8-oxo-guanosine-5'-diphosphateChEBI
8-oxo-2'-Deoxyguanosine-5'-diphosphateChEBI
8-Oxodeoxyguanosine diphosphateChEBI
2'-Deoxy-8-oxo-guanosine-5'-diphosphoric acidGenerator
8-oxo-2'-Deoxyguanosine-5'-diphosphoric acidGenerator
8-Oxodeoxyguanosine diphosphoric acidGenerator
2'-Deoxy-7,8-dihydro-8-oxoguanosine diphosphateHMDB
8-oxo-7,8-Dihydrodeoxyguanosine diphosphateHMDB
Chemical FormulaC10H15N5O11P2
Average Molecular Weight443.2005
Monoisotopic Molecular Weight443.024329371
IUPAC Name[({[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional Name{[(2R,3S,5R)-5-(6,8-dihydroxy-2-imino-3H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
[H][C@]1(O)C[C@@]([H])(O[C@]1([H])COP(O)(=O)OP(O)(O)=O)N1C(O)=NC2=C1NC(=N)N=C2O
InChI Identifier
InChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
InChI KeyLJMLTZSNWOCYNQ-VPENINKCSA-N
Chemical Taxonomy
Description 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
  • Purinone
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Alkyl phosphate
  • Vinylogous amide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Azole
  • Imidazole
  • Urea
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • 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
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
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
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC20176
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound49835950
PDB ID8GD
ChEBI ID63728
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.
Gene Name:
NUDT5
Uniprot ID:
Q9UKK9
Molecular weight:
24327.41
Reactions
8-oxo-dGDP + Water → 8-Oxo-dGMP + Phosphatedetails
General function:
Involved in hydrolase activity
Specific function:
Mediates the hydrolyzis of oxidized nucleoside diphosphate derivatives. Hydrolyzes 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to the monophosphates. Hydrolyzes 8-oxo-dGDP and 8-oxo-GDP with the same efficiencies. Hydrolyzes also 8-OH-dADP and 2-OH-dADP. Exhibited no or minimal hydrolyzis activity against 8-oxo-dGTP, 8-oxo-GTP, dGTP, GTP, dGDP and GDP. Probably removes oxidized guanine nucleotides from both the DNA and RNA precursor pools.
Gene Name:
NUDT18
Uniprot ID:
Q6ZVK8
Molecular weight:
35500.76
Reactions
8-oxo-dGDP + Water → 8-Oxo-dGMP + Phosphatedetails