zebularine   Click here for help

GtoPdb Ligand ID: 4729

PDB Ligand
Compound class: Synthetic organic

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2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 6
Hydrogen bond donors 3
Rotatable bonds 2
Topological polar surface area 104.81
Molecular weight 228.07
XLogP -0.9
No. Lipinski's rules broken 0

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES OCC1OC(C(C1O)O)n1cccnc1=O
Isomeric SMILES OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cccnc1=O
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
InChI Key RPQZTTQVRYEKCR-WCTZXXKLSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
Database Links Click here for help
CAS Registry No. 3690-10-6 (source: Scifinder)
ChEMBL Ligand CHEMBL504567
GtoPdb PubChem SID 178101440
PubChem CID 100016
RCSB PDB Ligand ZE8
Search Google for chemical match using the InChIKey RPQZTTQVRYEKCR-WCTZXXKLSA-N
Search Google for chemicals with the same backbone RPQZTTQVRYEKCR
UniChem Compound Search for chemical match using the InChIKey RPQZTTQVRYEKCR-WCTZXXKLSA-N
UniChem Connectivity Search for chemical match using the InChIKey RPQZTTQVRYEKCR-WCTZXXKLSA-N
Wikipedia Zebularine

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MedChemExpress
Zebularine (links to external site)
Cat. No. HY-13420