daptomycin   Click here for help

GtoPdb Ligand ID: 10904

Synonyms: Cubicin® | LY-146032 | LY146032
Approved drug
daptomycin is an approved drug (FDA (2003), EMA (2006))
Compound class: Synthetic organic
Comment: Daptomycin is a semi-synthetic cyclic lipopeptide antibacterial with broad-spectrum activity against Gram-positive bacteria. It is a bacterial metabolite that was isolated from Streptomyces roseosporus. Daptomycin rapidly depolarizes the bacterial cell membrane which disrupts DNA, RNA and protein synthesis and results in cell death.
This antibacterial was removed from the World Health Organization's List of Essential Medicines in 2019.
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 42
Hydrogen bond donors 22
Rotatable bonds 39
Topological polar surface area 702.02
Molecular weight 1619.71
XLogP 1.92
No. Lipinski's rules broken 3

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 NCCC[C@@H]1NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](Cc2c[nH]c3c2cccc3)NC(=O)CCCCCCCCC)CC(=O)N)CC(=O)O)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC1=O)CC(=O)O)C)CC(=O)O)CO)[C@@H](CC(=O)O)C)CC(=O)c1ccccc1N
Isomeric SMILES NCCC[C@@H]1NC(=O)CNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](Cc2c[nH]c3c2cccc3)NC(=O)CCCCCCCCC)CC(=O)N)CC(=O)O)[C@@H](C)OC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC1=O)CC(=O)O)C)CC(=O)O)CO)[C@@H](CC(=O)O)C)CC(=O)c1ccccc1N
InChI InChI=1S/C72H101N17O26/c1-5-6-7-8-9-10-11-22-53(93)81-44(25-38-31-76-42-20-15-13-17-39(38)42)66(108)84-45(27-52(75)92)67(109)86-48(30-59(102)103)68(110)89-61-37(4)115-72(114)49(26-51(91)40-18-12-14-19-41(40)74)87-71(113)60(35(2)24-56(96)97)88-69(111)50(34-90)82-55(95)32-77-63(105)46(28-57(98)99)83-62(104)36(3)79-65(107)47(29-58(100)101)85-64(106)43(21-16-23-73)80-54(94)33-78-70(61)112/h12-15,17-20,31,35-37,43-50,60-61,76,90H,5-11,16,21-30,32-34,73-74H2,1-4H3,(H2,75,92)(H,77,105)(H,78,112)(H,79,107)(H,80,94)(H,81,93)(H,82,95)(H,83,104)(H,84,108)(H,85,106)(H,86,109)(H,87,113)(H,88,111)(H,89,110)(H,96,97)(H,98,99)(H,100,101)(H,102,103)/t35-,36-,37-,43+,44+,45+,46+,47+,48+,49+,50-,60+,61+/m1/s1
InChI Key DOAKLVKFURWEDJ-RWDRXURGSA-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/)
Bioactivity Comments
MIC90 for antibacterial activity against erythromycin-nonsusceptible Streptococcus pyogenes is ≤30 ng/ml in vitro [1].