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daunorubicin   Click here for help

GtoPdb Ligand ID: 7063

Synonyms: Cerubidine® | daunomycin | FI-6339 | NDC-0082-4155 | RP-13057
Approved drug PDB Ligand
daunorubicin is an approved drug (FDA (1979), EMA (2018))
Compound class: Natural product
Comment: Daunorubicin is an anthracycline class chemotherapeutic for cancer treatment. It has also been shown to potentiate the activity of antibacterial agents of last resort, against multi-drug resistant (MDR) Gram-negative bacteria [1].
Daunorubicin is on the World Health Organisation's List of Essential Medicines.
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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Click here for structure editor
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 8
Hydrogen bond donors 5
Rotatable bonds 4
Topological polar surface area 185.84
Molecular weight 527.18
XLogP 0.56
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 COc1cccc2c1C(=O)c1c(C2=O)c(O)c2c(c1O)C(OC1CC(N)C(C(O1)C)O)CC(C2)(O)C(=O)C
Isomeric SMILES COc1cccc2c1C(=O)c1c(C2=O)c(O)c2c(c1O)[C@@H](O[C@H]1C[C@H](N)[C@@H]([C@@H](O1)C)O)C[C@](C2)(O)C(=O)C
InChI InChI=1S/C27H29NO10/c1-10-22(30)14(28)7-17(37-10)38-16-9-27(35,11(2)29)8-13-19(16)26(34)21-20(24(13)32)23(31)12-5-4-6-15(36-3)18(12)25(21)33/h4-6,10,14,16-17,22,30,32,34-35H,7-9,28H2,1-3H3/t10-,14-,16-,17-,22+,27-/m0/s1
InChI Key STQGQHZAVUOBTE-VGBVRHCVSA-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 Natural product
Approved drug? Yes. EU EMA (2018)  |  US FDA (1979)
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
(8S,10S)-8-acetyl-10-{[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-6,8,11-trihydroxy-1-methoxy-5,7,8,9,10,12-hexahydrotetracene-5,12-dione
International Nonproprietary Names Click here for help
INN number INN
2257 daunorubicin
Synonyms Click here for help
Cerubidine® | daunomycin | FI-6339 | NDC-0082-4155 | RP-13057
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Daunorubicin
Other databases
CAS Registry No. 20830-81-3 (source: Scifinder)
ChEBI CHEBI:41977
ChEMBL Ligand CHEMBL178
DrugBank Ligand DB00694
DrugCentral Ligand 786
GtoPdb PubChem SID 178103642
Immunopaedia Search daunorubicin
LIPID MAPS LMPK13050002
PubChem CID 30323
RCSB PDB Ligand DM1
Search Google for chemical match using the InChIKey STQGQHZAVUOBTE-VGBVRHCVSA-N
Search Google for chemicals with the same backbone STQGQHZAVUOBTE
Search PubMed clinical trials daunorubicin
Search PubMed titles daunorubicin
Search PubMed titles/abstracts daunorubicin
UniChem Compound Search for chemical match using the InChIKey STQGQHZAVUOBTE-VGBVRHCVSA-N
UniChem Connectivity Search for chemical match using the InChIKey STQGQHZAVUOBTE-VGBVRHCVSA-N
Wikipedia Daunorubicin