plitidepsin   Click here for help

GtoPdb Ligand ID: 11396

Synonyms: Aplidin® | aplidine | Dehydrodidemnin B
Approved drug PDB Ligand
plitidepsin is an approved drug
Compound class: Natural product or derivative
Comment: Plitidepsin was isolated from the sea squirt Aplidium albicans. It was found to have potent anti-tumour activity, that is mediated via modulation of human elongation factor 1-α (eEF1A) proteins and the translation process. Plitidepsin is also an immunomodulator and has antiviral properties.

SARS-CoV-2: The coronavirus exploits the eukaryotic (host) translation machinery to allow it to replicate. As a translation disruptor, plitidepsin has demonstrated in vivo anti-SARS-CoV-2 activity in mouse models of infection [1]. Under in vitro experimental conditions plitidepsin inhibited SARS-CoV-2 replication more effectively than remdesivir.
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 CDK toolkit. 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 21
Hydrogen bond donors 4
Rotatable bonds 18
Topological polar surface area 284.74
Molecular weight 1109.63
XLogP 5.07
No. Lipinski's rules broken 3
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.

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Canonical SMILES CC[C@@H]([C@H]1NC(=O)[C@@H](NC(=O)[C@H](N(C(=O)[C@@H]2CCCN2C(=O)C(=O)C)C)CC(C)C)[C@@H](C)OC(=O)[C@H](Cc2ccc(cc2)OC)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@@H](NC(=O)[C@H](C(=O)[C@@H](OC(=O)C[C@@H]1O)C(C)C)C)CC(C)C)C
Isomeric SMILES CC[C@@H]([C@H]1NC(=O)[C@@H](NC(=O)[C@H](N(C(=O)[C@@H]2CCCN2C(=O)C(=O)C)C)CC(C)C)[C@@H](C)OC(=O)[C@H](Cc2ccc(cc2)OC)N(C)C(=O)[C@@H]2CCCN2C(=O)[C@@H](NC(=O)[C@H](C(=O)[C@@H](OC(=O)C[C@@H]1O)C(C)C)C)CC(C)C)C
InChI InChI=1S/C57H87N7O15/c1-15-33(8)46-44(66)29-45(67)79-49(32(6)7)48(68)34(9)50(69)58-39(26-30(2)3)54(73)64-25-17-19-41(64)56(75)62(13)43(28-37-20-22-38(77-14)23-21-37)57(76)78-36(11)47(52(71)59-46)60-51(70)42(27-31(4)5)61(12)55(74)40-18-16-24-63(40)53(72)35(10)65/h20-23,30-34,36,39-44,46-47,49,66H,15-19,24-29H2,1-14H3,(H,58,69)(H,59,71)(H,60,70)/t33-,34-,36+,39-,40-,41-,42+,43-,44-,46+,47-,49-/m0/s1
InChI Key UUSZLLQJYRSZIS-LXNNNBEUSA-N
Bioactivity Comments
Plitidepsin inhibits replication of SARS-CoV-2 in vitro with an IC90 of 88 nM [1].