Zebularine
PubChem CID
100016
Structure
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.
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.
Chemical Structure Depiction
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)
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)
RPQZTTQVRYEKCR-WCTZXXKLSA-N
Computed by InChI 1.0.6 (PubChem release 2021.10.14)
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)
C9H12N2O5
Computed by PubChem 2.2 (PubChem release 2021.10.14)
- 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
- Zebularine
- 3690-10-6
- Pyrimidin-2-one ribonucleoside
- Pyrimidin-2-one beta-ribofuranoside
- 4-Deoxyuridine
- Pyrimidin-2-one beta-D-ribofuranoside
- CHEBI:46938
- 1-beta-D-ribofuranosyl-2(1H)-pyrimidinone
- 1-beta-D-ribofuranosylpyrimidin-2(1H)-one
- MFCD04973699
- 7A9Y5SX0GY
- 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
- 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
- NSC309132;4-Deoxyuridine
- 2-Pyrimidone-1-beta-D-riboside
- C9H12N2O5
- 1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one
- NSC-309132
- NSC 309132
- 2(1H)-Pyrimidinone, 1-beta-D-ribofuranosyl-
- 1-ss-D-Ribofuranosyl-2(1H)-pyrimidinone; 4-Deoxyuridine; NSC 309132; Pyrimidin-2-one ss-D-Ribofuranoside
- 2(1H)-Pyrimidinone, 1-.beta.-D-ribofuranosyl-
- 4pd7
- UNII-7A9Y5SX0GY
- URIDINE, 4-DEOXY-
- SCHEMBL13032
- pyrimidin-2-one-ribonucleoside
- CHEMBL504567
- GTPL4729
- DTXSID20958099
- RPQZTTQVRYEKCR-WCTZXXKLSA-N
- HMS3413C14
- HMS3677C14
- BDBM50226311
- HB1378
- 1-Pentofuranosylpyrimidin-2(1H)-one
- 4-Deoxy-3'-deoxy-3'-fluoro uridine
- AKOS024457033
- Zebularine, >=98% (HPLC), solid
- CS-3403
- DB03068
- 1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-Hydroxymethyl-Tetrahydro-Furan-2-yl)-1H-Pyrimidin-2-one
- NCGC00159549-02
- BP-58607
- DA-59262
- DHZ
- DS-11855
- HY-13420
- 1-beta-D-Ribofuranosyl-2(1H)-pyrimidino ne
- NS00011709
- 1-(beta-D-ribofuranosyl)pyrimidin-2(1H)-one
- PYRIMIDIN-2-ONE .BETA.-D-RIBOFURANOSIDE
- 1-(.BETA.-D-RIBOFURANOSYL)-2-PYRIMIDONE
- J-700277
- Q8068322
- 1-(beta-D-Ribofuranosyl)-1,2-dihydropyrimidin-2-one
- 1-.BETA.-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
- BRD-K87714311-001-01-9
- BRD-K87714311-001-02-7
- ZE8
Property Name
Property Value
Reference
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)
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
Follow these links to do a live 2D search or do a live 3D search for this compound, sorted by annotation score. This section is deprecated (see here for details), but these live search links provide equivalent functionality to the table that was previously shown here.
Same Connectivity Count
Same Parent, Connectivity Count
Same Parent, Exact Count
Mixtures, Components, and Neutralized Forms Count
Similar Compounds (2D)
Similar Conformers (3D)
Patents are available for this chemical structure:
https://patentscope.wipo.int/search/en/result.jsf?inchikey=RPQZTTQVRYEKCR-WCTZXXKLSA-N
- CAS Common ChemistryLICENSEThe 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/
- ChemIDplusChemIDplus Chemical Information Classificationhttps://pubchem.ncbi.nlm.nih.gov/source/ChemIDplus
- DrugBankLICENSECreative Common's Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/legalcode)https://www.drugbank.ca/legal/terms_of_useZebularinehttps://www.drugbank.ca/drugs/DB03068
- EPA DSSTox1-Pentofuranosylpyrimidin-2(1H)-onehttps://comptox.epa.gov/dashboard/DTXSID20958099CompTox Chemicals Dashboard Chemical Listshttps://comptox.epa.gov/dashboard/chemical-lists/
- FDA Global Substance Registration System (GSRS)LICENSEUnless 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
- ChEBI
- NCI Thesaurus (NCIt)LICENSEUnless 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-reuseNCI Thesaurushttps://ncit.nci.nih.gov
- ChEMBLLICENSEAccess 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.htmlChEMBL Protein Target Treehttps://www.ebi.ac.uk/chembl/g/#browse/targets
- Comparative Toxicogenomics Database (CTD)LICENSEIt 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.jsppyrimidin-2-one beta-ribofuranosidehttps://ctdbase.org/detail.go?type=chem&acc=C009131
- Drug Gene Interaction database (DGIdb)LICENSEThe 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/downloadsZEBULARINEhttps://www.dgidb.org/drugs/ncit:C37455
- Japan Chemical Substance Dictionary (Nikkaji)
- Metabolomics Workbench
- NORMAN Suspect List ExchangeLICENSEData: CC-BY 4.0; Code (hosted by ECI, LCSB): Artistic-2.0https://creativecommons.org/licenses/by/4.0/ZebularineNORMAN Suspect List Exchange Classificationhttps://www.norman-network.com/nds/SLE/
- Protein Data Bank in Europe (PDBe)
- RCSB Protein Data Bank (RCSB PDB)LICENSEData 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
- SpectraBase1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)-2-oxolanyl]-2-pyrimidinonehttps://spectrabase.com/spectrum/QkB1oA9oVN
- Springer Nature
- Wikidata4-deoxyuridinehttps://www.wikidata.org/wiki/Q8068322
- WikipediaNotholaenic acidhttps://en.wikipedia.org/wiki/Notholaenic_acidZebularinehttps://en.wikipedia.org/wiki/Zebularine
- PubChem
- Medical Subject Headings (MeSH)LICENSEWorks 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.htmlpyrimidin-2-one beta-ribofuranosidehttps://www.ncbi.nlm.nih.gov/mesh/67009131
- MolGenieMolGenie Organic Chemistry Ontologyhttps://github.com/MolGenie/ontology/
- PATENTSCOPE (WIPO)SID 388884460https://pubchem.ncbi.nlm.nih.gov/substance/388884460
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