puromycin   Click here for help

GtoPdb Ligand ID: 13311

Synonyms: achromycin
PDB Ligand
Compound class: Natural product
Comment: Puromycin is an aminoacyl nucleoside antimicrobial compound, originally isolated from Streptomyces alboniger [4]. It is a potent inhibitor of protein translation in both eukaryotic and prokaryotic organisms [5] and has not been of clinical utility due to its non-selective systemic toxicity. Instead it is used extensively in the laboratory to study mechanisms of protein synthesis and also as a selective agent in mammalian cell culture systems (reviewed in [2]).
Please note that puromycin was formerly known as achromycin, which was also a trade name used for tetracycline.
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species

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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 12
Hydrogen bond donors 4
Rotatable bonds 9
Topological polar surface area 157.6
Molecular weight 471.51
XLogP -1.28
No. Lipinski's rules broken 1

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 CN(C)C1=NC=NC2=C1N=CN2[C@H]3[C@@H]([C@@H]([C@@H](CO)O3)NC(=O)[C@H](CC4=CC=C(C=C4)OC)N)O
Isomeric SMILES CN(C)C1=NC=NC2=C1N=CN2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)NC(=O)[C@H](CC4=CC=C(C=C4)OC)N)O
InChI InChI=1S/C22H29N7O5/c1-28(2)19-17-20(25-10-24-19)29(11-26-17)22-18(31)16(15(9-30)34-22)27-21(32)14(23)8-12-4-6-13(33-3)7-5-12/h4-7,10-11,14-16,18,22,30-31H,8-9,23H2,1-3H3,(H,27,32)/t14-,15+,16+,18+,22+/m0/s1
InChI Key RXWNCPJZOCPEPQ-NVWDDTSBSA-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/)
References
1. Aeluri R, Ganji RJ, Marapaka AK, Pillalamarri V, Alla M, Addlagatta A. (2015)
Highly functionalized tetrahydropyridines are cytotoxic and selective inhibitors of human puromycin sensitive aminopeptidase.
Eur J Med Chem, 106: 26-33. [PMID:26513642]
2. Aviner R. (2020)
The science of puromycin: From studies of ribosome function to applications in biotechnology.
Comput Struct Biotechnol J, 18: 1074-1083. [PMID:32435426]
3. Vara JA, Portela A, Ortín J, Jiménez A. (1986)
Expression in mammalian cells of a gene from Streptomyces alboniger conferring puromycin resistance.
Nucleic Acids Res, 14 (11): 4617-24. [PMID:3714487]
4. Waller CW, Fryth PW, Hutchings BL, Williams JH. (1953)
Achromycin. The structure of the antibiotic puromycin. I.
J. Am. Chem. Soc., 75 (8): 2025. DOI: 10.1021/ja01104a537
5. Yarmolinsky MB, Haba GL. (1959)
INHIBITION BY PUROMYCIN OF AMINO ACID INCORPORATION INTO PROTEIN.
Proc Natl Acad Sci U S A, 45 (12): 1721-9. [PMID:16590564]