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2'-Deoxyadenosine

PubChem CID
13730
Structure
2'-Deoxyadenosine_small.png
2'-Deoxyadenosine_3D_Structure.png
Molecular Formula
Synonyms
  • 2'-deoxyadenosine
  • 958-09-8
  • deoxyadenosine
  • Adenyldeoxyriboside
  • Adenine deoxyribose
Molecular Weight
251.24 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-01-04
Description
2'-deoxyadenosine is a purine 2'-deoxyribonucleoside having adenine as the nucleobase. It has a role as a human metabolite, a Saccharomyces cerevisiae metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a purines 2'-deoxy-D-ribonucleoside and a purine 2'-deoxyribonucleoside.
Deoxyadenosine is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).
2'-Deoxyadenosine has been reported in Fritillaria przewalskii, Homo sapiens, and other organisms with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
2'-Deoxyadenosine.png

1.2 3D Conformer

1.3 Crystal Structures

COD records with this CID as component

2 Biologic Description

IUPAC Condensed
dAdo
Sequence
A
HELM
RNA1{[dR](A)}$$$$
IUPAC
2'-deoxy-adenosine

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-ol
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C10H13N5O3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(17)6(2-16)18-7/h3-7,16-17H,1-2H2,(H2,11,12,13)/t5-,6+,7+/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

OLXZPDWKRNYJJZ-RRKCRQDMSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.4 SMILES

C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(N=CN=C32)N)CO)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C10H13N5O3
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

40627-14-3
16373-93-6

3.3.2 Deprecated CAS

663188-78-1, 7005-15-4
96893-70-8
1348455-97-9, 663188-78-1, 7005-15-4

3.3.3 European Community (EC) Number

3.3.4 UNII

3.3.5 ChEBI ID

3.3.6 ChEMBL ID

3.3.7 DSSTox Substance ID

3.3.8 HMDB ID

3.3.9 KEGG ID

3.3.10 Metabolomics Workbench ID

3.3.11 NCI Thesaurus Code

3.3.12 Nikkaji Number

3.3.13 RXCUI

3.3.14 Wikidata

3.3.15 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • 2'-deoxyadenosine
  • 2-deoxyadenosine
  • deoxyadenosine

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
251.24 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3
Property Value
-0.5
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
3
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
7
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
2
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
251.10183929 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
251.10183929 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
119 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
18
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
307
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Isotope Atom Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Atom Stereocenter Count
Property Value
3
Reference
Computed by PubChem
Property Name
Undefined Atom Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Defined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Undefined Bond Stereocenter Count
Property Value
0
Reference
Computed by PubChem
Property Name
Covalently-Bonded Unit Count
Property Value
1
Reference
Computed by PubChem
Property Name
Compound Is Canonicalized
Property Value
Yes
Reference
Computed by PubChem (release 2021.10.14)

4.2 Experimental Properties

4.2.1 Physical Description

White odorless crystals; [La-Mar-Ka MSDS]
Solid

4.2.2 Melting Point

189 °C

4.2.3 LogP

-0.55
HANSCH,C ET AL. (1995)

4.2.4 Dissociation Constants

4.2.5 Collision Cross Section

152.3 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]

152.2 Ų [M-H]- [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]

154.6 Ų [M+H]+ [CCS Type: TW; Method: calibrated with polyalanine and drug standards]

162.73 Ų [M+H]+ [CCS Type: DT; Method: stepped-field]

166.67 Ų [M+Na]+ [CCS Type: DT; Method: stepped-field]

160.57 Ų [M-H]- [CCS Type: DT; Method: stepped-field]

151.59 Ų [M+H]+ [CCS Type: TW; Method: calibrated with polyalanine and drug standards]

161.34 Ų [M+K]+ [CCS Type: TW; Method: calibrated with polyalanine and drug standards]

156.61 Ų [M+Na]+ [CCS Type: TW; Method: calibrated with polyalanine and drug standards]

148.55 Ų [M+H-H2O]+ [CCS Type: TW; Method: calibrated with polyalanine and drug standards]

Ross et al. JASMS 2022; 33; 1061-1072. DOI:10.1021/jasms.2c00111

152.3 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

161.6 Ų [M+Na]+ [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

155.3 Ų [M-H]- [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

158.1 Ų [M+H]+ [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

155.4 Ų [M-H]-

158.2 Ų [M+H]+

152.3 Ų [M+H]+

161.9 Ų [M+Na]+

S50 | CCSCOMPEND | The Unified Collision Cross Section (CCS) Compendium | DOI:10.5281/zenodo.2658162

4.3 SpringerMaterials Properties

4.4 Chemical Classes

Biological Agents -> Nucleic Acids and Derivatives

5 Spectral Information

5.1 1D NMR Spectra

5.1.1 1H NMR Spectra

Spectra ID
Instrument Type
Varian
Frequency
600 MHz
Solvent
Water
pH
7.00
Shifts [ppm]:Intensity
3.80:30.90, 8.29:98.32, 4.65:19.46, 3.78:16.49, 2.57:13.08, 3.77:15.93, 4.64:18.73, 4.19:28.51, 3.79:30.19, 3.85:16.95, 2.55:11.11, 4.17:12.74, 6.46:21.73, 4.18:30.15, 4.19:11.78, 4.64:9.90, 2.57:13.56, 8.18:100.00, 2.83:12.79, 3.84:32.75, 2.79:12.28, 2.54:10.64, 2.55:11.29, 2.58:12.61, 2.54:10.97, 2.56:13.32, 2.84:10.61, 2.83:13.18, 2.82:21.94, 4.65:18.29, 6.43:22.14, 3.83:31.44, 2.81:14.56, 4.66:8.88, 2.80:16.01, 3.86:16.77, 6.44:32.14
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5.1.2 13C NMR Spectra

1 of 2
Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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2 of 2
Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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5.1.3 15N NMR Spectra

1 of 2
Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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2 of 2
Copyright
Copyright © 2016-2024 W. Robien, Inst. of Org. Chem., Univ. of Vienna. All Rights Reserved.
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5.2 2D NMR Spectra

5.2.1 1H-13C NMR Spectra

2D NMR Spectra Type
1H-13C HSQC
Spectra ID
Instrument Type
Bruker
Frequency
600 MHz
Solvent
Water
pH
7.00
Shifts [ppm] (F2:F1):Intensity
6.45:87.42:0.75, 3.83:64.42:0.64, 2.56:41.80:0.23, 4.18:90.24:1.00, 2.82:41.80:0.27, 4.64:74.11:0.79, 8.20:155.16:0.53, 3.79:64.42:0.60, 8.30:143.06:0.51
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5.3 Mass Spectrometry

5.3.1 GC-MS

1 of 11
View All
Spectra ID
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

207.0 100

192.0 99.90

103.0 80.48

208.0 63.36

236.0 33.73

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Notes
instrument=Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies
2 of 11
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Spectra ID
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

73.0 100

207.0 31.43

192.0 30.23

103.0 23.52

208.0 20.22

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Notes
instrument=Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies

5.3.2 MS-MS

1 of 6
View All
Spectra ID
Ionization Mode
Positive
Top 5 Peaks

136.0639 100

119.0382 38.36

45.03443 20.19

43.05404 14.12

73.02892 8.01

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Spectra ID
Ionization Mode
Positive
Top 5 Peaks

136.0621 100

117.0548 2.99

99.0446 2.98

119.0352 2.07

73.0297 2.07

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5.3.3 LC-MS

1 of 13
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Authors
da Silva KM, Iturrospe E, van de Lavoir M, Robeyns R, University of Antwerp, Belgium
Instrument
Agilent 6530 QTOF
Instrument Type
LC-ESI-QTOF
MS Level
MS2
Ionization Mode
POSITIVE
Ionization
ESI
Collision Energy
10 eV
Fragmentation Mode
CID
Retention Time
0.323 min
Precursor m/z
252.1091
Precursor Adduct
[M+H]+
Top 5 Peaks

136.0614 999

59.0473 126

252.111 85

117.0533 59

234.095 53

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License
CC BY
2 of 13
View All
Authors
Kakazu Y, Horai H, Institute for Advanced Biosciences, Keio Univ.
Instrument
API3000, Applied Biosystems
Instrument Type
LC-ESI-QQ
MS Level
MS2
Ionization Mode
POSITIVE
Collision Energy
10 V
Precursor m/z
252
Precursor Adduct
[M+H]+
Top 5 Peaks

252.3 999

235.2 590

123.2 384

136.2 378

113.3 242

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License
CC BY-NC-SA

5.3.4 Other MS

1 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
252.27
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
positive
Collision Energy
40
Top 5 Peaks

136 100

135 50.25

43 5.73

134 5.14

45 4.91

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MoNA ID
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
252.27
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
positive
Collision Energy
50
Top 5 Peaks

136 100

135 30.37

119 17.21

134 12.92

43 8.85

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7 Chemical Vendors

8 Drug and Medication Information

8.1 Biomarker Information

9 Food Additives and Ingredients

9.1 Associated Foods

10 Pharmacology and Biochemistry

10.1 MeSH Pharmacological Classification

Mutagens
Chemical agents that increase the rate of genetic mutation by interfering with the function of nucleic acids. A clastogen is a specific mutagen that causes breaks in chromosomes. (See all compounds classified as Mutagens.)
Antiviral Agents
Agents used in the prophylaxis or therapy of VIRUS DISEASES. Some of the ways they may act include preventing viral replication by inhibiting viral DNA polymerase; binding to specific cell-surface receptors and inhibiting viral penetration or uncoating; inhibiting viral protein synthesis; or blocking late stages of virus assembly. (See all compounds classified as Antiviral Agents.)

10.2 Human Metabolite Information

10.2.1 Tissue Locations

All Tissues

10.2.2 Cellular Locations

  • Cytoplasm
  • Extracellular
  • Lysosome
  • Nucleus

10.2.3 Metabolite Pathways

10.3 Biochemical Reactions

11 Use and Manufacturing

11.1 Uses

EPA CPDat Chemical and Product Categories
The Chemical and Products Database, a resource for exposure-relevant data on chemicals in consumer products, Scientific Data, volume 5, Article number: 180125 (2018), DOI:10.1038/sdata.2018.125

11.2 General Manufacturing Information

EPA TSCA Commercial Activity Status
Adenosine, 2'-deoxy-: INACTIVE

12 Safety and Hazards

12.1 Hazards Identification

12.1.1 GHS Classification

1 of 2
View All
Note
Pictograms displayed are for 66.7% (2 of 3) of reports that indicate hazard statements. This chemical does not meet GHS hazard criteria for 33.3% (1 of 3) of reports.
Pictogram(s)
Irritant
Signal
Warning
GHS Hazard Statements

H315 (66.7%): Causes skin irritation [Warning Skin corrosion/irritation]

H319 (66.7%): Causes serious eye irritation [Warning Serious eye damage/eye irritation]

H335 (66.7%): May cause respiratory irritation [Warning Specific target organ toxicity, single exposure; Respiratory tract irritation]

Precautionary Statement Codes

P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, and P501

(The corresponding statement to each P-code can be found at the GHS Classification page.)

ECHA C&L Notifications Summary

Aggregated GHS information provided per 3 reports by companies from 3 notifications to the ECHA C&L Inventory. Each notification may be associated with multiple companies.

Reported as not meeting GHS hazard criteria per 1 of 3 reports by companies. For more detailed information, please visit ECHA C&L website.

There are 2 notifications provided by 2 of 3 reports by companies with hazard statement code(s).

Information may vary between notifications depending on impurities, additives, and other factors. The percentage value in parenthesis indicates the notified classification ratio from companies that provide hazard codes. Only hazard codes with percentage values above 10% are shown.

12.1.2 Hazard Classes and Categories

Skin Irrit. 2 (66.7%)

Eye Irrit. 2A (66.7%)

STOT SE 3 (66.7%)

Acute Tox. 3 (100%)

12.1.3 Hazards Summary

Intraperitoneal LD50 (rat) > 800 mg/kg; [RTECS]

12.2 Regulatory Information

New Zealand EPA Inventory of Chemical Status
Adenosine, 2'-deoxy-: Does not have an individual approval but may be used under an appropriate group standard

13 Toxicity

13.1 Toxicological Information

13.1.1 Carcinogen Classification

Carcinogen Classification
No indication of carcinogenicity to humans (not listed by IARC).

13.1.2 Health Effects

Chronically high levels of deoxyadenosine are associated Adenosine Deaminase Deficiency.

13.1.3 Acute Effects

14 Associated Disorders and Diseases

Disease
Colorectal cancer
References

PubMed: 7482520, 19006102, 23940645, 24424155, 20156336, 19678709, 22148915, 25105552, 21773981, 25037050, 27015276, 27107423, 27275383, 28587349

Silke Matysik, Caroline Ivanne Le Roy, Gerhard Liebisch, Sandrine Paule Claus. Metabolomics of fecal samples: A practical consideration. Trends in Food Science & Technology. Vol. 57, Part B, Nov. 2016, p.244-255: http://www.sciencedirect.com/science/article/pii/S0924224416301984

Disease
Adenosine deaminase deficiency
References
Disease
Eosinophilic esophagitis
References
Mordechai, Hien, and David S. Wishart
Disease
Adenylosuccinate lyase deficiency
References

15 Literature

15.1 Consolidated References

15.2 NLM Curated PubMed Citations

15.3 Springer Nature References

15.4 Thieme References

15.5 Wiley References

15.6 Nature Journal References

15.7 Chemical Co-Occurrences in Literature

15.8 Chemical-Gene Co-Occurrences in Literature

15.9 Chemical-Disease Co-Occurrences in Literature

16 Patents

16.1 Depositor-Supplied Patent Identifiers

16.2 WIPO PATENTSCOPE

16.3 Chemical Co-Occurrences in Patents

16.4 Chemical-Disease Co-Occurrences in Patents

16.5 Chemical-Gene Co-Occurrences in Patents

17 Interactions and Pathways

17.1 Protein Bound 3D Structures

17.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

17.2 Chemical-Target Interactions

17.3 Pathways

18 Biological Test Results

18.1 BioAssay Results

19 Taxonomy

WormJam Metabolites Local CSV for MetFrag | DOI:10.5281/zenodo.3403364
WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series, Worm, 6:2, e1373939, DOI:10.1080/21624054.2017.1373939
The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

20 Classification

20.1 MeSH Tree

20.2 NCI Thesaurus Tree

20.3 ChEBI Ontology

20.4 KEGG: Metabolite

20.5 ChemIDplus

20.6 ChEMBL Target Tree

20.7 UN GHS Classification

20.8 EPA CPDat Classification

20.9 NORMAN Suspect List Exchange Classification

20.10 CCSBase Classification

20.11 EPA DSSTox Classification

20.12 EPA TSCA and CDR Classification

20.13 LOTUS Tree

20.14 EPA Substance Registry Services Tree

20.15 MolGenie Organic Chemistry Ontology

21 Information Sources

  1. CAS Common Chemistry
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  2. ChemIDplus
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    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. EPA Chemicals under the TSCA
    EPA TSCA Classification
    https://www.epa.gov/tsca-inventory
  4. EPA DSSTox
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. European Chemicals Agency (ECHA)
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  7. Human Metabolome Database (HMDB)
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  9. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  10. NORMAN Suspect List Exchange
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    https://creativecommons.org/licenses/by/4.0/
    Deoxyadenosine
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  11. ChEBI
  12. E. coli Metabolome Database (ECMDB)
    LICENSE
    ECMDB is offered to the public as a freely available resource.
    https://ecmdb.ca/citations
  13. LOTUS - the natural products occurrence database
    LICENSE
    The code for LOTUS is released under the GNU General Public License v3.0.
    https://lotus.nprod.net/
  14. NCI Thesaurus (NCIt)
    LICENSE
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  15. Toxin and Toxin Target Database (T3DB)
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  16. Yeast Metabolome Database (YMDB)
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    http://www.ymdb.ca/downloads
  17. ChEMBL
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    http://www.ebi.ac.uk/Information/termsofuse.html
  18. Comparative Toxicogenomics Database (CTD)
    LICENSE
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    http://ctdbase.org/about/legal.jsp
  19. Crystallography Open Database (COD)
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    https://creativecommons.org/publicdomain/zero/1.0/
  20. ECI Group, LCSB, University of Luxembourg
    LICENSE
    Data: CC-BY 4.0; Code: Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    2'-deoxyadenosine
  21. Natural Product Activity and Species Source (NPASS)
  22. EPA Chemical and Products Database (CPDat)
  23. FooDB
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    https://foodb.ca/about
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    https://haz-map.com/About
  25. MassBank Europe
  26. MassBank of North America (MoNA)
    LICENSE
    The content of the MoNA database is licensed under CC BY 4.0.
    https://mona.fiehnlab.ucdavis.edu/documentation/license
  27. SpectraBase
    6-AMINO-9-(2-DEOXY-BETA-D-ERYTHRO-PENTOFURANOSYL)-PURINE
    https://spectrabase.com/spectrum/44lTVPK30kL
  28. IUPAC Digitized pKa Dataset
  29. Japan Chemical Substance Dictionary (Nikkaji)
  30. KEGG
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  31. MarkerDB
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  32. Metabolomics Workbench
  33. Nature Chemical Biology
  34. NLM RxNorm Terminology
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  36. RCSB Protein Data Bank (RCSB PDB)
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  37. Rhea - Annotated Reactions Database
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  46. GHS Classification (UNECE)
  47. EPA Substance Registry Services
  48. MolGenie
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  49. PATENTSCOPE (WIPO)
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