Human Metabolome Database Version 3.5

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 | PDB | 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 Reference
Urine Detected and Quantified
1.00 (0.00-2.00) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
<1.0 umol/mmol creatinine Adult (>18 years old) Not Specified Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 11.0 (2.0-20.0) uM Adult (>18 years old) Both Purine nucleoside phosphorylase (PNP) deficiency
Urine Detected and Quantified 177.0-322.0 umol/mmol creatinine Adult (>18 years old) Not Specified Purine Nucleoside Phosphorylase Deficiency
Associated Disorders and Diseases
Disease References
Purine nucleoside phosphorylase deficiency
  • 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
  • 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
      Associated OMIM IDs
      • 164050 Link_out (Purine nucleoside phosphorylase deficiency )
      DrugBank ID Not Available
      DrugBank Metabolite 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: 5'-nucleotidase
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5E
      Uniprot ID: P21589 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic 5'-nucleotidase 1B
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5C1B
      Uniprot ID: Q96P26 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic 5'-nucleotidase 1A
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5C1A
      Uniprot ID: Q9BXI3 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 5'(3')-deoxyribonucleotidase, cytosolic type
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5C
      Uniprot ID: Q8TCD5 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: 5'(3')-deoxyribonucleotidase, mitochondrial
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5M
      Uniprot ID: Q9NPB1 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Deoxyguanosine kinase, mitochondrial
      Reactions:
      Adenosine triphosphate + Deoxyguanosine unknown ADP + 2'-Deoxyguanosine 5'-monophosphate details
      Gene Name: DGUOK
      Uniprot ID: Q16854 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic 5'-nucleotidase 3
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5C3
      Uniprot ID: Q9H0P0 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Cytosolic purine 5'-nucleotidase
      Reactions:
      2'-Deoxyguanosine 5'-monophosphate + Water unknown Deoxyguanosine + Phosphoric acid details
      Gene Name: NT5C2
      Uniprot ID: P49902 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA
      Name: Purine nucleoside phosphorylase
      Reactions:
      Deoxyguanosine + Phosphoric acid unknown Guanine + Deoxyribose 1-phosphate details
      Gene Name: PNP
      Uniprot ID: P00491 Link_out
      Protein Sequence: FASTA
      Gene Sequence: FASTA