cytarabine   Click here for help

GtoPdb Ligand ID: 4827

Synonyms: Cytosar® | DepoCyte® | U-19920
Approved drug PDB Ligand
cytarabine is an approved drug (FDA (1969), EMA (2001))
Compound class: Synthetic organic
Comment: Cytarabine is an antimetabolite antineoplastic agent that inhibits the synthesis of DNA.
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-CCXZUQQUSA-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
Approved drug? Yes (FDA (1969), EMA (2001))
WHO Essential Medicine WHO Essential Medicines List (EML) (23rd List, 2023). Access PDF version.
Click to view more information about the WHO Model Lists of Essential Medicines.
IUPAC Name Click here for help
4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
International Nonproprietary Names Click here for help
INN number INN
1709 cytarabine
Synonyms Click here for help
Cytosar® | DepoCyte® | U-19920
Database Links Click here for help
CAS Registry No. 147-94-4 (source: Scifinder)
ChEMBL Ligand CHEMBL803
DrugBank Ligand DB00987
DrugCentral Ligand 770
GtoPdb PubChem SID 178101529
PubChem CID 6253
RCSB PDB Ligand AR3
Search Google for chemical match using the InChIKey UHDGCWIWMRVCDJ-CCXZUQQUSA-N
Search Google for chemicals with the same backbone UHDGCWIWMRVCDJ
Search PubMed clinical trials cytarabine
Search PubMed titles cytarabine
Search PubMed titles/abstracts cytarabine
UniChem Compound Search for chemical match using the InChIKey UHDGCWIWMRVCDJ-CCXZUQQUSA-N
UniChem Connectivity Search for chemical match using the InChIKey UHDGCWIWMRVCDJ-CCXZUQQUSA-N
Wikipedia Cytarabine