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Zebularine

PubChem CID
100016
Structure
Zebularine_small.png
Zebularine_3D_Structure.png
Molecular Formula
Synonyms
  • Zebularine
  • 3690-10-6
  • Pyrimidin-2-one ribonucleoside
  • Pyrimidin-2-one beta-ribofuranoside
  • 4-Deoxyuridine
Molecular Weight
228.20 g/mol
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Dates
  • Create:
    2005-06-24
  • Modify:
    2025-01-18
Description
Zebularine is a member of pyrimidine ribonucleosides.
A chemically stable, cytidine analog that displays anti-tumor properties. It acts as a transition state analog inhibitor of cytidine deaminase by binding to the active site as covalent hydrates. Also shown to inhibit DNA methylation and tumor growth both in vitro and in vivo.
Zebularine is a synthetic cytidine analogue and a cytidine deaminase inhibitor with anticancer activity. Following metabolic activation by phosphorylation and incorporation into DNA, zebularine inhibits DNA methyltransferase through covalent complex formation between the enzyme and zebularine-substituted DNA, hence resulting in non-specific, genome-wide induction of demethylation including the removal of aberrant methylation of promoter regions of genes critical for normal cellular functions.

1 Structures

1.1 2D Structure

Chemical Structure Depiction
Zebularine.png

1.2 3D Conformer

2 Names and Identifiers

2.1 Computed Descriptors

2.1.1 IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
Computed by Lexichem TK 2.7.0 (PubChem release 2021.10.14)

2.1.2 InChI

InChI=1S/C9H12N2O5/c12-4-5-6(13)7(14)8(16-5)11-3-1-2-10-9(11)15/h1-3,5-8,12-14H,4H2/t5-,6-,7-,8-/m1/s1
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.3 InChIKey

RPQZTTQVRYEKCR-WCTZXXKLSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)

2.1.4 SMILES

C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
Computed by OEChem 2.3.0 (PubChem release 2024.12.12)

2.2 Molecular Formula

C9H12N2O5
Computed by PubChem 2.2 (PubChem release 2021.10.14)

2.3 Other Identifiers

2.3.1 CAS

2.3.2 UNII

2.3.3 ChEBI ID

2.3.4 ChEMBL ID

2.3.5 DrugBank ID

2.3.6 DSSTox Substance ID

2.3.7 Metabolomics Workbench ID

2.3.8 NCI Thesaurus Code

2.3.9 Nikkaji Number

2.3.10 Wikidata

2.3.11 Wikipedia

2.4 Synonyms

2.4.1 MeSH Entry Terms

  • 4-deoxyuridine
  • NSC 309132
  • pyrimidin-2-one beta-D-ribofuranoside
  • pyrimidin-2-one beta-ribofuranoside
  • pyrimidin-2-one beta-ribofuranoside, (L)-isomer
  • pyrimidin-2-one ribonucleoside
  • zebularine

2.4.2 Depositor-Supplied Synonyms

3 Chemical and Physical Properties

3.1 Computed Properties

Property Name
Molecular Weight
Property Value
228.20 g/mol
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
XLogP3
Property Value
-1.5
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
5
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
228.07462149 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Monoisotopic Mass
Property Value
228.07462149 Da
Reference
Computed by PubChem 2.2 (PubChem release 2021.10.14)
Property Name
Topological Polar Surface Area
Property Value
103 Ų
Reference
Computed by Cactvs 3.4.8.18 (PubChem release 2021.10.14)
Property Name
Heavy Atom Count
Property Value
16
Reference
Computed by PubChem
Property Name
Formal Charge
Property Value
0
Reference
Computed by PubChem
Property Name
Complexity
Property Value
343
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
4
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)

3.2 Chemical Classes

3.2.1 Drugs

Pharmaceuticals -> Antibiotics
S6 | ITNANTIBIOTIC | Antibiotic List from the ITN MSCA ANSWER | DOI:10.5281/zenodo.2621956
Pharmaceuticals -> Listed in ZINC15
S55 | ZINC15PHARMA | Pharmaceuticals from ZINC15 | DOI:10.5281/zenodo.3247749

4 Spectral Information

4.1 Mass Spectrometry

4.1.1 GC-MS

Source of Spectrum
KO-23-436-5
Copyright
Copyright © 2020-2024 John Wiley & Sons, Inc. All Rights Reserved.
Thumbnail
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6 Chemical Vendors

7 Associated Disorders and Diseases

8 Literature

8.1 Consolidated References

8.2 NLM Curated PubMed Citations

8.3 Springer Nature References

8.4 Chemical Co-Occurrences in Literature

8.5 Chemical-Gene Co-Occurrences in Literature

8.6 Chemical-Disease Co-Occurrences in Literature

9 Patents

9.1 Depositor-Supplied Patent Identifiers

9.2 WIPO PATENTSCOPE

9.3 Chemical Co-Occurrences in Patents

9.4 Chemical-Disease Co-Occurrences in Patents

9.5 Chemical-Gene Co-Occurrences in Patents

10 Interactions and Pathways

10.1 Protein Bound 3D Structures

10.1.1 Ligands from Protein Bound 3D Structures

PDBe Ligand Code
PDBe Structure Code
PDBe Conformer

10.2 Chemical-Target Interactions

10.3 Pathways

11 Biological Test Results

11.1 BioAssay Results

12 Classification

12.1 MeSH Tree

12.2 NCI Thesaurus Tree

12.3 ChEBI Ontology

12.4 ChemIDplus

12.5 ChEMBL Target Tree

12.6 NORMAN Suspect List Exchange Classification

12.7 EPA DSSTox Classification

12.8 MolGenie Organic Chemistry Ontology

13 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
  4. EPA DSSTox
    1-Pentofuranosylpyrimidin-2(1H)-one
    https://comptox.epa.gov/dashboard/DTXSID20958099
    CompTox Chemicals Dashboard Chemical Lists
    https://comptox.epa.gov/dashboard/chemical-lists/
  5. FDA Global Substance Registration System (GSRS)
    LICENSE
    Unless otherwise noted, the contents of the FDA website (www.fda.gov), both text and graphics, are not copyrighted. They are in the public domain and may be republished, reprinted and otherwise used freely by anyone without the need to obtain permission from FDA. Credit to the U.S. Food and Drug Administration as the source is appreciated but not required.
    https://www.fda.gov/about-fda/about-website/website-policies#linking
  6. ChEBI
  7. NCI Thesaurus (NCIt)
    LICENSE
    Unless otherwise indicated, all text within NCI products is free of copyright and may be reused without our permission. Credit the National Cancer Institute as the source.
    https://www.cancer.gov/policies/copyright-reuse
  8. 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
  9. 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
    pyrimidin-2-one beta-ribofuranoside
    https://ctdbase.org/detail.go?type=chem&acc=C009131
  10. Drug Gene Interaction database (DGIdb)
    LICENSE
    The data used in DGIdb is all open access and where possible made available as raw data dumps in the downloads section.
    http://www.dgidb.org/downloads
  11. Japan Chemical Substance Dictionary (Nikkaji)
  12. Metabolomics Workbench
  13. 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/
    Zebularine
    NORMAN Suspect List Exchange Classification
    https://www.norman-network.com/nds/SLE/
  14. Protein Data Bank in Europe (PDBe)
  15. 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
  16. SpectraBase
    1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-2-oxolanyl]-2-pyrimidinone
    https://spectrabase.com/spectrum/QkB1oA9oVN
  17. Springer Nature
  18. Wikidata
  19. Wikipedia
  20. PubChem
  21. 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
    pyrimidin-2-one beta-ribofuranoside
    https://www.ncbi.nlm.nih.gov/mesh/67009131
  22. MolGenie
    MolGenie Organic Chemistry Ontology
    https://github.com/MolGenie/ontology/
  23. PATENTSCOPE (WIPO)
CONTENTS