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2'-Deoxycytidine 5'-Triphosphate

PubChem CID
65091
Structure
2'-Deoxycytidine 5'-Triphosphate_small.png
2'-Deoxycytidine 5'-Triphosphate_3D_Structure.png
Molecular Formula
Synonyms
  • dCTP
  • Deoxycytidine triphosphate
  • 2056-98-6
  • 2'-Deoxycytidine 5'-triphosphate
  • Deoxycytidine 5'-triphosphate
Molecular Weight
467.16 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2004-09-16
  • Modify:
    2025-02-01
Description
DCTP is a 2'-deoxycytidine phosphate having cytosine as the nucleobase. It has a role as a human metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a 2'-deoxycytidine phosphate and a pyrimidine 2'-deoxyribonucleoside 5'-triphosphate. It is a conjugate acid of a dCTP(3-).
dCTP is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).
Deoxycytidine 5'-triphosphate is a metabolite found in or produced by Escherichia coli (strain K12, MG1655).

1 Structures

1.1 2D Structure

Chemical Structure Depiction
2'-Deoxycytidine 5'-Triphosphate.png

1.2 3D Conformer

2 Biologic Description

IUPAC Condensed
P-P-P-dCyd
Sequence
C
HELM
RNA1{[*P(=O)(O)OP(=O)(O)OP(=O)(O)O |$_R2;;;;;;;;;;;;|][dR](C)}$$$$
IUPAC
5'-triphospho-2'-deoxy-cytidine

3 Names and Identifiers

3.1 Computed Descriptors

3.1.1 IUPAC Name

[[(2R,3S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

3.1.2 InChI

InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

3.1.3 InChIKey

RGWHQCVHVJXOKC-SHYZEUOFSA-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=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

3.2 Molecular Formula

C9H16N3O13P3
Computed by PubChem 2.2 (PubChem release 2021.10.14)

3.3 Other Identifiers

3.3.1 CAS

102783-51-7

3.3.2 European Community (EC) Number

3.3.3 ChEBI ID

3.3.4 ChEMBL ID

3.3.5 DrugBank ID

3.3.6 DSSTox Substance ID

3.3.7 HMDB ID

3.3.8 KEGG ID

3.3.9 Metabolomics Workbench ID

3.3.10 Nikkaji Number

3.3.11 Wikidata

3.3.12 Wikipedia

3.4 Synonyms

3.4.1 MeSH Entry Terms

  • 2'-deoxycytidine 5'-triphosphate
  • 2'-deoxycytidine 5'-triphosphate, 3H-labeled
  • 2'-deoxycytidine 5'-triphosphate, magnesium salt
  • 2'-deoxycytidine 5'-triphosphate, P''-(32)P-labeled
  • 2'-deoxycytidine 5'-triphosphate, P-(32)P-labeled
  • dCTP
  • deoxycytidine triphosphate

3.4.2 Depositor-Supplied Synonyms

4 Chemical and Physical Properties

4.1 Computed Properties

Property Name
Molecular Weight
Property Value
467.16 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3
Property Value
-5.6
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
13
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Rotatable Bond Count
Property Value
8
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Exact Mass
Property Value
466.98959857 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
466.98959857 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
248 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
28
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
823
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 Collision Cross Section

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

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

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 GC-MS

1 of 3
View All
Spectra ID
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

160.0 100

89.0 12.01

161.0 11.51

179.0 11.31

100.0 9.41

Thumbnail
Thumbnail
Notes
instrument=Leco Pegasus IV
2 of 3
View All
MS Category
Experimental
MS Type
GC-MS
MS Level
MS1
Instrument
Leco Pegasus IV
Instrument Type
GC-EI-TOF
Ionization Mode
positive
Top 5 Peaks

160 100

89 12.01

161 11.51

179 11.31

100 9.41

Thumbnail
Thumbnail

5.1.2 MS-MS

1 of 6
View All
Spectra ID
Instrument Type
Orbitrap
Ionization Mode
negative
Top 5 Peaks

465.9832 81.99

158.9258 12.15

368.0061 4.73

466.9863 1.13

Thumbnail
Thumbnail
Notes
adduct_type [M-H]- original_collision_energy 18 nominal CannabisDB spectra from NIST14 2020 June Thermo Finnigan Elite Orbitrap
2 of 6
View All
Spectra ID
Instrument Type
Orbitrap
Ionization Mode
negative
Top 5 Peaks

465.983 40.42

158.9258 35.96

368.0061 12.51

386.0166 3.21

176.9363 1.92

Thumbnail
Thumbnail
Notes
adduct_type [M-H]- original_collision_energy 23 nominal CannabisDB spectra from NIST14 2020 June Thermo Finnigan Elite Orbitrap

5.1.3 Other MS

MoNA ID
MS Category
Experimental
MS Type
Other
MS Level
MS2
Precursor Type
[M+H]+
Precursor m/z
468.04
Instrument
TQD, Waters
Instrument Type
Flow-injection QqQ/MS
Ionization
ESI
Ionization Mode
positive
Collision Energy
30
Top 5 Peaks
370 100
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 Safety and Hazards

10.1 Hazards Identification

10.1.1 GHS Classification

Note
This chemical does not meet GHS hazard criteria for 100% (2 of 2) of all reports. Pictograms displayed are for < 0.1% (0 of 2) of reports that indicate hazard statements.
GHS Hazard Statements

Not Classified

Reported as not meeting GHS hazard criteria by 2 of 2 companies. For more detailed information, please visit ECHA C&L website.

ECHA C&L Notifications Summary

Aggregated GHS information provided per 2 reports by companies from 1 notifications to the ECHA C&L Inventory.

Reported as not meeting GHS hazard criteria per 2 of 2 reports by companies. For more detailed information, please visit ECHA C&L website.

There are 0 notifications provided by 0 of 2 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.

10.1.2 Hazard Classes and Categories

Not Classified

11 Literature

11.1 Consolidated References

11.2 NLM Curated PubMed Citations

11.3 Springer Nature References

11.4 Nature Journal References

11.5 Chemical Co-Occurrences in Literature

11.6 Chemical-Gene Co-Occurrences in Literature

11.7 Chemical-Disease Co-Occurrences in Literature

12 Patents

12.1 Depositor-Supplied Patent Identifiers

12.2 WIPO PATENTSCOPE

12.3 Chemical Co-Occurrences in Patents

12.4 Chemical-Disease Co-Occurrences in Patents

12.5 Chemical-Gene Co-Occurrences in Patents

13 Interactions and Pathways

13.1 Protein Bound 3D Structures

13.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

13.2 Chemical-Target Interactions

13.3 Pathways

14 Biological Test Results

14.1 BioAssay Results

15 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

16 Classification

16.1 MeSH Tree

16.2 ChEBI Ontology

16.3 KEGG: Metabolite

16.4 ChemIDplus

16.5 ChEMBL Target Tree

16.6 UN GHS Classification

16.7 NORMAN Suspect List Exchange Classification

16.8 CCSBase Classification

16.9 EPA DSSTox Classification

16.10 LOTUS Tree

16.11 MolGenie Organic Chemistry Ontology

17 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. ChemIDplus
    ChemIDplus Chemical Information Classification
    https://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
  3. 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'-Deoxycytidine 5'-triphosphate
    https://www.drugbank.ca/drugs/DB03258
  4. EPA DSSTox
    2'-Deoxycytidine 5'-(tetrahydrogen triphosphate)
    https://comptox.epa.gov/dashboard/DTXSID60942755
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. European Chemicals Agency (ECHA)
    LICENSE
    Use of the information, documents and data from the ECHA website is subject to the terms and conditions of this Legal Notice, and subject to other binding limitations provided for under applicable law, the information, documents and data made available on the ECHA website may be reproduced, distributed and/or used, totally or in part, for non-commercial purposes provided that ECHA is acknowledged as the source: "Source: European Chemicals Agency, http://echa.europa.eu/". Such acknowledgement must be included in each copy of the material. ECHA permits and encourages organisations and individuals to create links to the ECHA website under the following cumulative conditions: Links can only be made to webpages that provide a link to the Legal Notice page.
    https://echa.europa.eu/web/guest/legal-notice
    Cytidine 5'-(tetrahydrogen triphosphate), 2'-deoxy-
    https://echa.europa.eu/substance-information/-/substanceinfo/100.016.504
    Cytidine 5'-(tetrahydrogen triphosphate), 2'-deoxy-, disodium salt
    https://echa.europa.eu/substance-information/-/substanceinfo/100.119.225
    Cytidine 5'-(tetrahydrogen triphosphate), 2'-deoxy-, disodium salt (EC: 600-356-2)
    https://echa.europa.eu/information-on-chemicals/cl-inventory-database/-/discli/details/64613
  6. 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
  7. CCSbase
    CCSbase Classification
    https://ccsbase.net/
  8. ChEBI
  9. E. coli Metabolome Database (ECMDB)
    LICENSE
    ECMDB is offered to the public as a freely available resource.
    https://ecmdb.ca/citations
  10. 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'-Deoxycytidine-5'-triphosphate
    https://www.wikidata.org/wiki/Q424680
  11. Yeast Metabolome Database (YMDB)
    LICENSE
    YMDB is offered to the public as a freely available resource.
    http://www.ymdb.ca/downloads
  12. 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
  13. Comparative Toxicogenomics Database (CTD)
    LICENSE
    It is to be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of NC State University.
    http://ctdbase.org/about/legal.jsp
  14. ECI Group, LCSB, University of Luxembourg
    LICENSE
    Data: CC-BY 4.0; Code: Artistic-2.0
    https://creativecommons.org/licenses/by/4.0/
    dCTP
  15. Natural Product Activity and Species Source (NPASS)
  16. 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
  17. 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
  18. Japan Chemical Substance Dictionary (Nikkaji)
  19. 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
  20. Metabolomics Workbench
  21. Nature Chemical Biology
  22. 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/
    Deoxycytidine triphosphate
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  23. Protein Data Bank in Europe (PDBe)
  24. 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
  25. Springer Nature
  26. Wikidata
  27. Wikipedia
  28. PubChem
  29. Medical Subject Headings (MeSH)
    LICENSE
    Works produced by the U.S. government are not subject to copyright protection in the United States. Any such works found on National Library of Medicine (NLM) Web sites may be freely used or reproduced without permission in the U.S.
    https://www.nlm.nih.gov/copyright.html
    2'-deoxycytidine 5'-triphosphate
    https://www.ncbi.nlm.nih.gov/mesh/67024107
  30. GHS Classification (UNECE)
  31. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  32. PATENTSCOPE (WIPO)
  33. NCBI
CONTENTS