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Human Metabolome Database Version 3.5

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Showing metabocard for Deoxyguanosine (HMDB00085)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:07:52 -0700
HMDB ID HMDB00085
Secondary Accession Numbers None
Metabolite Identification
Common Name Deoxyguanosine
Description Deoxyguanosine is a nucleoside consisting of the base guanine and the sugar deoxyribose. It is like guanosine, but with one oxygen atom removed. It is a nucleoside component of DNA. Deoxyguanosine can be converted to 8-hydroxy-deoxyguanosine (8-OHdG) due to hydroxyl radical attack at the C8 of guanine. 8-OHdG is a sensitive marker of the DNA damage This damage, if left unrepaired, has been proposed to contribute to mutagenicity and cancer promotion.
Structure Thumb
Download: MOL | SDF | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 2'-Deoxy-Guanosine
  2. 2'-Deoxyguanosine
  3. 2-Deoxyguanosine
  4. 9-(2-Deoxy-b-D-erythro-pentofuranosyl)-Guanine
  5. 9-(2-Deoxy-b-D-erythro-pentofuranosyl)guanine
  6. 9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-Guanine
  7. 9-(2-Deoxy-beta-delta-erythro-pentofuranosyl)guanine
  8. Deoxyguanosine
  9. Desoxyguanosine
  10. Guanine deoxy nucleoside
  11. Guanine deoxyriboside
Chemical Formula C10H13N5O4
Average Molecular Weight 267.2413
Monoisotopic Molecular Weight 267.096753929
IUPAC Name 2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-one
Traditional IUPAC Name 2'-deoxyguanosine
CAS Registry Number 961-07-9
SMILES NC1=NC2=C(N=CN2[C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)N1
InChI Identifier InChI=1S/C10H13N5O4/c11-10-13-8-7(9(18)14-10)12-3-15(8)6-1-4(17)5(2-16)19-6/h3-6,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5+,6+/m0/s1
InChI Key YKBGVTZYEHREMT-KVQBGUIXSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Purine Nucleosides and Analogues
Sub Class Purine 2'-deoxyribonucleosides and Analogues
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • a deoxynucleoside(Cyc)
  • a purine-related compound(Cyc)
Substituents
  • Aminopyrimidine
  • Hypoxanthine
  • Imidazole
  • Imidazopyrimidine
  • Oxolane
  • Primary Alcohol
  • Purine
  • Purinone
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct Parent Purine 2'-deoxyribonucleosides and Analogues
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
Application Not Available
Cellular locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 300 °C Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP -1.30 BALZARINI,JM ET AL. (1989)
Predicted Properties
Property Value Source
Water Solubility 11.5 g/L ALOGPS
LogP -1.75 ALOGPS
LogP -1.8 ChemAxon
LogS -1.37 ALOGPS
pKa (strongest acidic) 10.16 ChemAxon
pKa (strongest basic) 1.83 ChemAxon
Hydrogen Acceptor Count 7 ChemAxon
Hydrogen Donor Count 4 ChemAxon
Polar Surface Area 134.99 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 63.11 ChemAxon
Polarizability 25.22 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
Gas-MS Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies)
MS/MS Spectrum LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies)
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • All Tissues
Pathways
Name SMPDB Link KEGG Link
Purine Metabolism SMP00050 map00230 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Comments
Urine Detected and Quantified
Article_icon
1.00 (0.00-2.00) umol/mmol creatinine Adult (>18 years old) Both Normal Not Available
Urine Detected and Quantified
Article_icon
<1.0 umol/mmol creatinine Adult (>18 years old) Not Specified Normal Not Available
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Comments
Blood Detected and Quantified
Article_icon
11.0 (2.0-20.0) uM Adult (>18 years old) Both Purine nucleoside phosphorylase (PNP) deficiency Not Available
Urine Detected and Quantified
Article_icon
177.0-322.0 umol/mmol creatinine Adult (>18 years old) Not Specified Purine Nucleoside Phosphorylase Deficiency Not Available
Associated Disorders and Diseases
Disease References
Purine nucleoside phosphorylase deficiency
  • Gandhi V, Kilpatrick JM, Plunkett W, Ayres M, Harman L, Du M, Bantia S, Davisson J, Wierda WG, Faderl S, Kantarjian H, Thomas D: A proof-of-principle pharmacokinetic, pharmacodynamic, and clinical study with purine nucleoside phosphorylase inhibitor immucillin-H (BCX-1777, forodesine). Blood. 2005 Dec 15;106(13):4253-60. Epub 2005 Aug 30. Pubmed: 16131572 Link_out
  • Wevers RA, Engelke UF, Moolenaar SH, Brautigam C, de Jong JG, Duran R, de Abreu RA, van Gennip AH: 1H-NMR spectroscopy of body fluids: inborn errors of purine and pyrimidine metabolism. Clin Chem. 1999 Apr;45(4):539-48. Pubmed: 10102915 Link_out
    Associated OMIM IDs
    • 164050 Link_out (Purine nucleoside phosphorylase deficiency )
    DrugBank ID Not Available
    Phenol Explorer Compound ID Not Available
    Phenol Explorer Metabolite ID Not Available
    FoodDB ID FDB012064
    KNApSAcK ID Not Available
    Chemspider ID 163230 Link_out
    KEGG Compound ID C00330 Link_out
    BioCyc ID DEOXYGUANOSINE Link_out
    BiGG ID 34637 Link_out
    Wikipedia Link Deoxyguanosine Link_out
    NuGOwiki Link HMDB00085 Link_out
    Metagene Link HMDB00085 Link_out
    METLIN ID 3395 Link_out
    PubChem Compound 187790 Link_out
    PDB ID GNG Link_out
    ChEBI ID 17172 Link_out
    References
    Synthesis Reference Noguchi, Toshitada; Hamamoto, Tomoki; Okuyama, Kiyoshi; Shibuya, Susumu. Process for producing 2'-deoxyguanosine. PCT Int. Appl. (2003), 31 pp.
    Material Safety Data Sheet (MSDS) Download (PDF)
    General References
    1. Gao K, Henning SM, Niu Y, Youssefian AA, Seeram NP, Xu A, Heber D: The citrus flavonoid naringenin stimulates DNA repair in prostate cancer cells. J Nutr Biochem. 2006 Feb;17(2):89-95. Epub 2005 Jun 20. Pubmed: 16111881 Link_out
    2. Podmore K, Farmer PB, Herbert KE, Jones GD, Martin EA: 32P-postlabelling approaches for the detection of 8-oxo-2'-deoxyguanosine-3'-monophosphate in DNA. Mutat Res. 1997 Aug 1;378(1-2):139-49. Pubmed: 9288892 Link_out
    3. Shibata T, Iio K, Kawai Y, Shibata N, Kawaguchi M, Toi S, Kobayashi M, Kobayashi M, Yamamoto K, Uchida K: Identification of a lipid peroxidation product as a potential trigger of the p53 pathway. J Biol Chem. 2006 Jan 13;281(2):1196-204. Epub 2005 Oct 26. Pubmed: 16251187 Link_out
    4. Gackowski D, Ciecierski M, Jawien A, Olinski R: Background level of 8-oxo-2'-deoxyguanosine in lymphocyte DNA does not correlate with the concentration of antioxidant vitamins in blood plasma. Acta Biochim Pol. 2001;48(2):535-9. Pubmed: 11732622 Link_out
    5. Takamura-Enya T, Watanabe M, Totsuka Y, Kanazawa T, Matsushima-Hibiya Y, Koyama K, Sugimura T, Wakabayashi K: Mono(ADP-ribosyl)ation of 2'-deoxyguanosine residue in DNA by an apoptosis-inducing protein, pierisin-1, from cabbage butterfly. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12414-9. Epub 2001 Oct 9. Pubmed: 11592983 Link_out
    6. Palozza P, Serini S, Di Nicuolo F, Boninsegna A, Torsello A, Maggiano N, Ranelletti FO, Wolf FI, Calviello G, Cittadini A: beta-Carotene exacerbates DNA oxidative damage and modifies p53-related pathways of cell proliferation and apoptosis in cultured cells exposed to tobacco smoke condensate. Carcinogenesis. 2004 Aug;25(8):1315-25. Epub 2004 Apr 8. Pubmed: 15073048 Link_out
    7. Zaidi SN, Laidlaw I, Howell A, Potten CS, Cooper DP, O'Connor PJ: Normal human breast xenografts activate N-nitrosodimethylamine: identification of potential target cells for an environmental nitrosamine. Br J Cancer. 1992 Jul;66(1):79-83. Pubmed: 1637681 Link_out
    8. Gackowski D, Banaszkiewicz Z, Rozalski R, Jawien A, Olinski R: Persistent oxidative stress in colorectal carcinoma patients. Int J Cancer. 2002 Oct 1;101(4):395-7. Pubmed: 12209966 Link_out
    9. Araki S, Hayashi M, Tamagawa K, Saito M, Kato S, Komori T, Sakakihara Y, Mizutani T, Oda M: Neuropathological analysis in spinal muscular atrophy type II. Acta Neuropathol (Berl). 2003 Nov;106(5):441-8. Epub 2003 Jul 25. Pubmed: 12898156 Link_out
    10. Kato I, Ren J, Heilbrun LK, Djuric Z: Intra- and inter-individual variability in measurements of biomarkers for oxidative damage in vivo: Nutrition and Breast Health Study. Biomarkers. 2006 Mar-Apr;11(2):143-52. Pubmed: 16766390 Link_out
    11. Izzedine H, Launay-Vacher V, Aymard G, Legrand M, Deray G: Pharmacokinetics of abacavir in HIV-1-infected patients with impaired renal function. Nephron. 2001 Sep;89(1):62-7. Pubmed: 11528234 Link_out
    12. Wevers RA, Engelke UF, Moolenaar SH, Brautigam C, de Jong JG, Duran R, de Abreu RA, van Gennip AH: 1H-NMR spectroscopy of body fluids: inborn errors of purine and pyrimidine metabolism. Clin Chem. 1999 Apr;45(4):539-48. Pubmed: 10102915 Link_out
    13. Bowen P, Chen L, Stacewicz-Sapuntzakis M, Duncan C, Sharifi R, Ghosh L, Kim HS, Christov-Tzelkov K, van Breemen R: Tomato sauce supplementation and prostate cancer: lycopene accumulation and modulation of biomarkers of carcinogenesis. Exp Biol Med (Maywood). 2002 Nov;227(10):886-93. Pubmed: 12424330 Link_out
    14. Staal GE, Stoop JW, Zegers BJ, Siegenbeek van Heukelom LH, van der Vlist MJ, Wadman SK, Martin DW: Erythrocyte metabolism in purine nucleoside phosphorylase deficiency after enzyme replacement therapy by infusion of erythrocytes. J Clin Invest. 1980 Jan;65(1):103-8. Pubmed: 6765955 Link_out
    15. Blair IA: Lipid hydroperoxide-mediated DNA damage. Exp Gerontol. 2001 Sep;36(9):1473-81. Pubmed: 11525870 Link_out
    16. Schramm VL: Development of transition state analogues of purine nucleoside phosphorylase as anti-T-cell agents. Biochim Biophys Acta. 2002 Jul 18;1587(2-3):107-17. Pubmed: 12084452 Link_out
    17. Schilderman PA, Rhijnsburger E, Zwingmann I, Kleinjans JC: Induction of oxidative DNA damages and enhancement of cell proliferation in human lymphocytes in vitro by butylated hydroxyanisole. Carcinogenesis. 1995 Mar;16(3):507-12. Pubmed: 7697806 Link_out
    18. Kaneko T, Tahara S: Formation of 8-oxo-2'-deoxyguanosine in the DNA of human diploid fibroblasts by treatment with linoleic acid hydroperoxide and ferric ion. Lipids. 2000 Sep;35(9):961-5. Pubmed: 11026616 Link_out
    19. Hou SM, Nori P, Fang JL, Vaca CE: Methylglyoxal induces hprt mutation and DNA adducts in human T-lymphocytes in vitro. Environ Mol Mutagen. 1995;26(4):286-91. Pubmed: 8575417 Link_out
    20. Bialkowski K, Kowara R, Windorbska W, Olinski R: 8-Oxo-2'-deoxyguanosine level in lymphocytes DNA of cancer patients undergoing radiotherapy. Cancer Lett. 1996 Jan 19;99(1):93-7. Pubmed: 8564935 Link_out
    Enzymes
    Name: Cytosolic 5'-nucleotidase 1B
    Reactions:
    • a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate [RN:R07297]
    Gene Name: NT5C1B
    Uniprot ID: Q96P26 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: Cytosolic 5'-nucleotidase 1A
    Reactions:
    • a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate [RN:R07297]
    Gene Name: NT5C1A
    Uniprot ID: Q9BXI3 Link_out
    Protein Sequence: FASTA
    Gene Sequence: FASTA
    Name: 5'(3')-deoxyribonucleotidase, cytosolic type
    Reactions:
      Gene Name: NT5C
      Uniprot ID: Q8TCD5 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 5'(3')-deoxyribonucleotidase, mitochondrial
      Reactions:
        Gene Name: NT5M
        Uniprot ID: Q9NPB1 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Deoxyguanosine kinase, mitochondrial
        Reactions:
        • ATP + deoxyguanosine = ADP + dGMP [RN:R01967]
        Gene Name: DGUOK
        Uniprot ID: Q16854 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA
        Name: Cytosolic 5'-nucleotidase 3
        Reactions:
        • a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate [RN:R07297]
        Gene Name: NT5C3
        Uniprot ID: Q9H0P0 Link_out
        Protein Sequence: FASTA
        Gene Sequence: FASTA