cytidine   Click here for help

GtoPdb Ligand ID: 4728

PDB Ligand
Compound class: Metabolite

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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 7
Hydrogen bond donors 4
Rotatable bonds 2
Topological polar surface area 130.83
Molecular weight 243.09
XLogP -0.98
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)n1ccc(nc1=O)N
Isomeric SMILES OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1ccc(nc1=O)N
InChI InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChI Key UHDGCWIWMRVCDJ-XVFCMESISA-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 Metabolite
IUPAC Name Click here for help
4-amino-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. 65-46-3 (source: Scifinder)
ChEBI CHEBI:17562
ChEMBL Ligand CHEMBL95606
DrugBank Ligand DB02097
GtoPdb PubChem SID 178101439
PubChem CID 6175
RCSB PDB Ligand CTN
Search Google for chemical match using the InChIKey UHDGCWIWMRVCDJ-XVFCMESISA-N
Search Google for chemicals with the same backbone UHDGCWIWMRVCDJ
UniChem Compound Search for chemical match using the InChIKey UHDGCWIWMRVCDJ-XVFCMESISA-N
UniChem Connectivity Search for chemical match using the InChIKey UHDGCWIWMRVCDJ-XVFCMESISA-N
Wikipedia Cytidine

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MedChemExpress
Cytidine (links to external site)
Cat. No. HY-B0158