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2'-Deoxyguanosine-5'-diphosphate

PubChem CID
135398595
Structure
2'-Deoxyguanosine-5'-diphosphate_small.png
Molecular Formula
Synonyms
  • dGDP
  • 2'-deoxyguanosine-5'-diphosphate
  • 3493-09-2
  • CHEBI:28862
  • 2'-Deoxyguanosine 5'-diphosphate
Molecular Weight
427.20 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2019-01-15
  • Modify:
    2025-01-18
Description
DGDP is a purine 2'-deoxyribonucleoside 5'-diphosphate having guanine as the nucleobase. It has a role as a fundamental metabolite. It is a purine 2'-deoxyribonucleoside 5'-diphosphate, a guanyl deoxyribonucleotide and a deoxyguanosine phosphate. It is a conjugate acid of a dGDP(3-).
dGDP is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).
2'-Deoxyguanosine-5'-diphosphate has been reported in Homo sapiens with data available.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
2'-Deoxyguanosine-5'-diphosphate.png

1.2 3D Status

Conformer generation failed at generation step

2 Biologic Description

IUPAC Condensed
P-P-dGuo
Sequence
G
HELM
RNA1{[*P(=O)(O)OP(=O)(O)O |$_R2;;;;;;;;|][dR](G)}$$$$
IUPAC
5'-diphospho-2'-deoxy-guanosine

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

CIKGWCTVFSRMJU-KVQBGUIXSA-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=C2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C10H15N5O10P2
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

3.3.2 ChEBI ID

3.3.3 ChEMBL ID

3.3.4 DrugBank ID

3.3.5 DSSTox Substance ID

3.3.6 HMDB ID

3.3.7 KEGG ID

3.3.8 Metabolomics Workbench ID

3.3.9 Nikkaji Number

3.3.10 Wikidata

3.3.11 Wikipedia

3.4 Synonyms

3.4.1 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
427.20 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3-AA
Property Value
-4.5
Reference
Computed by XLogP3 3.0 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Donor Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Hydrogen Bond Acceptor Count
Property Value
12
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
6
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
427.02941569 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
427.02941569 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
228 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
27
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
729
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

Solid

4.2.2 Solubility

5.5 mg/mL

4.2.3 Collision Cross Section

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

174.28 Ų [M-H2O-H]- [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]

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

185.6 Ų [M+Na-2H]- [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

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

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

177.5 Ų [M+Na-2H]- [CCS Type: DT; Method: single field calibrated with ESI Low Concentration Tuning Mix (Agilent)]

177.4 Ų [M-2H+Na]-

185.7 Ų [M-2H+Na]-

180.8 Ų [M-H]-

185.1 Ų [M+Na]+

188.5 Ų [M+H]+

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

4.3 Chemical Classes

4.3.1 Drugs

Pharmaceuticals -> Listed in ZINC15
S55 | ZINC15PHARMA | Pharmaceuticals from ZINC15 | DOI:10.5281/zenodo.3247749

5 Spectral Information

5.1 Mass Spectrometry

5.1.1 MS-MS

1 of 6
View All
Spectra ID
Instrument Type
LC-ESI-QTOF
Ionization Mode
negative
Top 5 Peaks

78.9603 50.45

426.0216 45.59

158.9266 38.71

Thumbnail
Thumbnail
Notes
instrument=UPLC Q-Tof Premier, Waters
2 of 6
View All
Spectra ID
Ionization Mode
positive
Top 5 Peaks

152.056549 100

81.034004 18.64

87.092079 5.05

113.107422 4.94

281.152191 4.82

Thumbnail
Thumbnail
Notes
instrument=Q-Exactive Plus

5.1.2 LC-MS

1 of 4
View All
Authors
Matsuda F, Suzuki M, Sawada Y, Plant Science Center, RIKEN.
Instrument
UPLC Q-Tof Premier, Waters
Instrument Type
LC-ESI-QTOF
MS Level
MS2
Ionization Mode
NEGATIVE
Ionization
ESI
Collision Energy
Ramp 5-60 V
Fragmentation Mode
LOW-ENERGY CID
Precursor m/z
426.02162
Precursor Adduct
[M-H]-
Top 5 Peaks

78.9603 999

426.0216 903

158.9266 767

Thumbnail
Thumbnail
License
CC BY-SA
2 of 4
View All
MoNA ID
MS Category
Experimental
MS Type
LC-MS
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
426.02162
Instrument
UPLC Q-Tof Premier, Waters
Instrument Type
LC-ESI-QTOF
Ionization
ESI
Ionization Mode
negative
Collision Energy
Ramp 5-60 V
Top 5 Peaks

78.9603 50.45

426.0216 45.59

158.9266 38.71

Thumbnail
Thumbnail
License
CC BY-SA

5.1.3 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
428.31
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
positive
Collision Energy
50
Top 5 Peaks

152 100

151 20.51

81 6.80

Thumbnail
Thumbnail
2 of 3
View All
MoNA ID
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M-H]-
Precursor m/z
426.32
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
negative
Collision Energy
20
Top 5 Peaks

426 100

425 19.52

427 14.33

Thumbnail
Thumbnail

7 Chemical Vendors

8 Food Additives and Ingredients

8.1 Associated Foods

9 Pharmacology and Biochemistry

9.1 Human Metabolite Information

9.1.1 Cellular Locations

  • Cytoplasm
  • Mitochondria
  • Nucleus

9.1.2 Metabolite Pathways

9.2 Biochemical Reactions

10 Literature

10.1 Consolidated References

10.2 Springer Nature References

10.3 Chemical Co-Occurrences in Literature

10.4 Chemical-Gene Co-Occurrences in Literature

10.5 Chemical-Disease Co-Occurrences in Literature

11 Patents

11.1 Depositor-Supplied Patent Identifiers

11.2 WIPO PATENTSCOPE

11.3 Chemical Co-Occurrences in Patents

11.4 Chemical-Disease Co-Occurrences in Patents

11.5 Chemical-Gene Co-Occurrences in Patents

12 Interactions and Pathways

12.1 Protein Bound 3D Structures

12.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

12.2 Chemical-Target Interactions

12.3 Pathways

13 Biological Test Results

13.1 BioAssay Results

14 Taxonomy

The LOTUS Initiative for Open Natural Products Research: frozen dataset union wikidata (with metadata) | DOI:10.5281/zenodo.5794106

15 Classification

15.1 ChEBI Ontology

15.2 KEGG: Metabolite

15.3 ChEMBL Target Tree

15.4 NORMAN Suspect List Exchange Classification

15.5 CCSBase Classification

15.6 EPA DSSTox Classification

15.7 LOTUS Tree

15.8 MolGenie Organic Chemistry Ontology

16 Information Sources

  1. CAS Common Chemistry
    LICENSE
    The data from CAS Common Chemistry is provided under a CC-BY-NC 4.0 license, unless otherwise stated.
    https://creativecommons.org/licenses/by-nc/4.0/
  2. EPA DSSTox
    [(2R,3S,5R)-5-(2-Amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methyl phosphono hydrogen phosphate
    https://comptox.epa.gov/dashboard/DTXSID601027110
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  3. Human Metabolome Database (HMDB)
    LICENSE
    HMDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (HMDB) and the original publication (see the HMDB citing page). We ask that users who download significant portions of the database cite the HMDB paper in any resulting publications.
    http://www.hmdb.ca/citing
  4. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  5. NORMAN Suspect List Exchange
    LICENSE
    Data: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    Dgdp | 2'-deoxy-gdp
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  6. ChEBI
  7. E. coli Metabolome Database (ECMDB)
    LICENSE
    ECMDB is offered to the public as a freely available resource.
    https://ecmdb.ca/citations
  8. 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/
    2'-Deoxyguanosine-5'-diphosphate
    https://www.wikidata.org/wiki/Q27103932
  9. Yeast Metabolome Database (YMDB)
    LICENSE
    YMDB is offered to the public as a freely available resource.
    http://www.ymdb.ca/downloads
  10. ChEMBL
    LICENSE
    Access to the web interface of ChEMBL is made under the EBI's Terms of Use (http://www.ebi.ac.uk/Information/termsofuse.html). The ChEMBL data is made available on a Creative Commons Attribution-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-sa/3.0/).
    http://www.ebi.ac.uk/Information/termsofuse.html
  11. DrugBank
    LICENSE
    Creative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)
    https://www.drugbank.ca/legal/terms_of_use
    2'-Deoxyguanosine-5'-Diphosphate
    https://www.drugbank.ca/drugs/DB03491
  12. FooDB
    LICENSE
    FooDB is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (FooDB) and the original publication.
    https://foodb.ca/about
  13. Japan Chemical Substance Dictionary (Nikkaji)
  14. KEGG
    LICENSE
    Academic users may freely use the KEGG website. Non-academic use of KEGG generally requires a commercial license
    https://www.kegg.jp/kegg/legal.html
  15. MassBank Europe
  16. 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
  17. Metabolomics Workbench
  18. Protein Data Bank in Europe (PDBe)
  19. RCSB Protein Data Bank (RCSB PDB)
    LICENSE
    Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Users of the data should attribute the original authors of that structural data.
    https://www.rcsb.org/pages/policies
  20. Springer Nature
  21. Wikidata
  22. Wikipedia
  23. PubChem
  24. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  25. PATENTSCOPE (WIPO)
CONTENTS