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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-20 22:13:26 UTC
Update Date2021-09-14 15:44:42 UTC
HMDB IDHMDB0001786
Secondary Accession Numbers
  • HMDB01786
Metabolite Identification
Common NameEthenodeoxyadenosine
DescriptionEtheno nucleosides are a new class of chemically modified components of nucleic acids. These base-modified nucleosides demonstrate significant biological properties, acting, among others, as antiviral or antitumor agents. One of the possible modifications of the nucleoside is their transformation into ethenonucleosides. Thus, nucleosides or their respective heterocyclic bases, possessing an exocyclic amino group, as well as a neighboring endocyclic nitrogen, can react with some bifunctional reagents (e.g., α-halocarbonyl compounds) to form products with an additional five-membered ring of the imidazole type. The ethenonucleosides basically do not occur in nature; some of the only exceptions are Y-nucleosides. Etheno modified DNA bases are generated from the carcinogens vinyl chloride and urethane, but also by reactions of DNA with products derived from lipid peroxidation (LPO) and oxidative stress via endogenous pathways. Highly variable background levels of epsilon-adducts were detected in DNA from different organs of unexposed humans and rodents. Several known cancer risk factors increased the level of these DNA lesions in target organs: elevated epsilon-adducts were found in hepatic DNA from patients with metal storage diseases, after overproduction of nitric oxide (NO) by inducible NO synthase (iNOS) in a mouse model, and in colonic polyps of familial adenomatous polyposis patients. A high omega-6-polyunsaturated fatty acid diet increased epsilon-DNA adducts in white blood cells of female subjects. (PMID:10882861 ).
Structure
Data?1582752211
Synonyms
ValueSource
1,N(6)-DeoxyethenoadenosineMeSH
1,N(6)-EthenodeoxyadenosineMeSH
1,N2-Etheno-2'-deoxyguanosineMeSH
1,N6-Etheno-2'-deoxyadenosineMeSH
2'-Deoxy-2-deuteroethenoadenosineMeSH
1,N6-etheno-DAHMDB
1,N6-EthenodeoxyadenosineHMDB
N1,N6-etheno-2'-DeoxyadenosineHMDB
Chemical FormulaC12H13N5O3
Average Molecular Weight275.2633
Monoisotopic Molecular Weight275.101839307
IUPAC Name(2R,3S,5R)-2-(hydroxymethyl)-5-{3H-imidazo[2,1-f]purin-3-yl}oxolan-3-ol
Traditional Nameethenodeoxyadenosine
CAS Registry Number68498-25-9
SMILES
OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C21
InChI Identifier
InChI=1S/C12H13N5O3/c18-4-8-7(19)3-9(20-8)17-6-14-10-11-13-1-2-16(11)5-15-12(10)17/h1-2,5-9,18-19H,3-4H2/t7-,8+,9+/m0/s1
InChI KeyXQQIMTUYVDUWKJ-DJLDLDEBSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as purines and purine derivatives. These are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyrimidines
Sub ClassPurines and purine derivatives
Direct ParentPurines and purine derivatives
Alternative Parents
Substituents
  • Purine
  • N-substituted imidazole
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Imidazole
  • Azole
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot 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
PropertyValueSource
Water Solubility5.98 g/LALOGPS
logP-1.1ALOGPS
logP-1.4ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)13.89ChemAxon
pKa (Strongest Basic)4.96ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area97.7 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity68.08 m³·mol⁻¹ChemAxon
Polarizability27.1 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+160.50331661259
DarkChem[M-H]-160.60931661259
AllCCS[M+H]+163.11332859911
AllCCS[M-H]-164.29132859911
DeepCCS[M-2H]-187.32330932474
DeepCCS[M+Na]+162.53230932474
AllCCS[M+H]+163.132859911
AllCCS[M+H-H2O]+159.632859911
AllCCS[M+NH4]+166.432859911
AllCCS[M+Na]+167.432859911
AllCCS[M-H]-164.332859911
AllCCS[M+Na-2H]-163.632859911
AllCCS[M+HCOO]-162.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
EthenodeoxyadenosineOC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C213268.0Standard polar33892256
EthenodeoxyadenosineOC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C212433.1Standard non polar33892256
EthenodeoxyadenosineOC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CN1C=CN=C212913.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Ethenodeoxyadenosine,1TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O2871.0Semi standard non polar33892256
Ethenodeoxyadenosine,1TMS,isomer #2C[Si](C)(C)O[C@H]1C[C@H](N2C=NC3=C2N=CN2C=CN=C32)O[C@@H]1CO2870.0Semi standard non polar33892256
Ethenodeoxyadenosine,2TMS,isomer #1C[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O[Si](C)(C)C2871.5Semi standard non polar33892256
Ethenodeoxyadenosine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O3086.1Semi standard non polar33892256
Ethenodeoxyadenosine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](N2C=NC3=C2N=CN2C=CN=C32)O[C@@H]1CO3087.4Semi standard non polar33892256
Ethenodeoxyadenosine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1O[C@@H](N2C=NC3=C2N=CN2C=CN=C32)C[C@@H]1O[Si](C)(C)C(C)(C)C3292.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Ethenodeoxyadenosine GC-MS (Non-derivatized) - 70eV, Positivesplash10-054o-9170000000-59787ef95e13965a6f742017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ethenodeoxyadenosine GC-MS (2 TMS) - 70eV, Positivesplash10-0v4i-9855100000-1aa19e03cd5abf43bec22017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Ethenodeoxyadenosine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Ethenodeoxyadenosine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-004i-0090000000-1cbcf897b8d539f74c9d2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ethenodeoxyadenosine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-03di-0900000000-7351b3ecaf69532e4ae92012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Ethenodeoxyadenosine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-03di-1900000000-cea99433c51ea3b57b8c2012-07-24HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Positive-QTOFsplash10-03di-0920000000-4723a3e7bccfd3fb82a32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Positive-QTOFsplash10-03di-0900000000-319e0450fd20aa8b295f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Positive-QTOFsplash10-03di-0900000000-123c329a87834ac8c7192017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Negative-QTOFsplash10-00di-0290000000-8d53e894625170dfa26f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Negative-QTOFsplash10-0a4i-0910000000-c8a7d5a2ae45462ace752017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Negative-QTOFsplash10-0a4i-0900000000-944674f1809414d8aa982017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Positive-QTOFsplash10-03di-0900000000-491bffd5eb2009008d642021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Positive-QTOFsplash10-03di-0900000000-491bffd5eb2009008d642021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Positive-QTOFsplash10-03di-0900000000-d0145665222b050d7b7c2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 10V, Negative-QTOFsplash10-00di-0190000000-bf4918a4b52f776c05be2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 20V, Negative-QTOFsplash10-0a4i-0900000000-9997b969fd66d57e38892021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Ethenodeoxyadenosine 40V, Negative-QTOFsplash10-0a4i-0900000000-614f89543dcac00da2392021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-29Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)2012-12-05Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
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 IDFDB022701
KNApSAcK IDNot Available
Chemspider ID9120894
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6339
PubChem Compound10945668
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceSchmid K; Nair J; Winde G; Velic I; Bartsch H Increased levels of promutagenic etheno-DNA adducts in colonic polyps of FAP patients. International journal of cancer. Journal international du cancer (2000), 87(1), 1-4.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Hanaoka T, Nair J, Takahashi Y, Sasaki S, Bartsch H, Tsugane S: Urinary level of 1,N(6) -ethenodeoxyadenosine, a marker of oxidative stress, is associated with salt excretion and omega 6-polyunsaturated fatty acid intake in postmenopausal Japanese women. Int J Cancer. 2002 Jul 1;100(1):71-5. [PubMed:12115589 ]
  2. Hillestrom PR, Nyssonen K, Tuomainen TP, Pukkala E, Salonen JT, Poulsen HE: Urinary excretion of epsilondA is not predictive of cancer development: a prospective nested case-control study. Free Radic Res. 2005 Jan;39(1):51-3. [PubMed:15875811 ]
  3. Bartsch H, Nair J: New DNA-based biomarkers for oxidative stress and cancer chemoprevention studies. Eur J Cancer. 2000 Jun;36(10):1229-34. [PubMed:10882861 ]