clindamycin   Click here for help

GtoPdb Ligand ID: 10607

Approved drug PDB Ligand Antimalarial Ligand
clindamycin is an approved drug (FDA (1970))
Compound class: Synthetic organic
Comment: Clindamycin is a semisynthetic lincosamide antibacterial with broad-spectrum activity. The compound also has antimalarial activity.
Clindamycin is one of the key access group antibacterials on the World Health Organization's Model List of Essential Medicines (link provided in the Classification table, under the Summary tab below).

The Malaria tab on this ligand page provides additional curator comments of relevance to the Guide to MALARIA PHARMACOLOGY.
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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
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 7
Hydrogen bond donors 4
Rotatable bonds 8
Topological polar surface area 127.56
Molecular weight 424.18
XLogP 2
No. Lipinski's rules broken 0
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 CCC[C@H]1CN([C@@H](C1)C(=O)N[C@@H]([C@H]1O[C@H](SC)[C@@H]([C@H]([C@H]1O)O)O)[C@@H](Cl)C)C
Isomeric SMILES CCC[C@H]1CN([C@@H](C1)C(=O)N[C@@H]([C@H]1O[C@H](SC)[C@@H]([C@H]([C@H]1O)O)O)[C@@H](Cl)C)C
InChI InChI=1S/C18H33ClN2O5S/c1-5-6-10-7-11(21(3)8-10)17(25)20-12(9(2)19)16-14(23)13(22)15(24)18(26-16)27-4/h9-16,18,22-24H,5-8H2,1-4H3,(H,20,25)/t9-,10+,11-,12+,13-,14+,15+,16+,18+/m0/s1
InChI Key KDLRVYVGXIQJDK-AWPVFWJPSA-N
Bioactivity Comments
Clindamycin, like a number of other antibacterials including azithromycin and doxycycline, kills the malaria parasite in the lifecycle after treatment starts [1]. Consistent with this slow clinical action, the results provided in the table below show that clindamycin is more potent in vitro against erythrocytic stage parasites when assessed two asexual life cycles after the initiation of treatment.
Whole organism assay data
Key to terms and symbols Click on species/strain names for details Click column headers to sort
MOA/likely target Sp. Assay description Type Action Value Parameter Concentration range (M) Reference
Unknown MOA PfW2

Plasmodium falciparum W2

P. falciparum strain W2 (PfW2) was cloned from the Indochina III/CDC isolate, originally derived from a Laotian patient who failed chloroquine therapy.
PfW2 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4) and is reported to be resistant to chloroquine and susceptible to mefloquine.
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 Ring formation assay (96 hours) - - 8.5 pIC50 - 1
⤷ pIC50 8.5 (IC50 3.12x10-9 M) FACS analysis following 96 hours in culture (third-generation rings) [1]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)
Unknown MOA Pf3D7

Plasmodium falciparum 3D7

P. falciparum strain 3D7 (Pf3D7) was derived from isolate NF54 by limiting dilution. The complete genome of Pf3D7 has been sequenced (GenBank: LN999946.1).
Pf3D7 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4) and is sensitive to a panel of antimalarial compounds including chloroquine and pyrimethamine.
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 Ring formation assay (96 hours) - - 8.1 pIC50 - 1
⤷ pIC50 8.1 (IC50 8.81x10-9 M) FACS analysis following 96 hours in culture (third-generation rings) [1]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)
Unknown MOA Pf3D7

Plasmodium falciparum 3D7

P. falciparum strain 3D7 (Pf3D7) was derived from isolate NF54 by limiting dilution. The complete genome of Pf3D7 has been sequenced (GenBank: LN999946.1).
Pf3D7 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4) and is sensitive to a panel of antimalarial compounds including chloroquine and pyrimethamine.
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 Ring formation assay (48 hours) - - <4.0 pIC50 - 1
⤷ pIC50 <4.0 (IC50 >1x10-4 M) FACS analysis following 48 hours in culture (second-generation rings) [1]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)
Unknown MOA PfW2

Plasmodium falciparum W2

P. falciparum strain W2 (PfW2) was cloned from the Indochina III/CDC isolate, originally derived from a Laotian patient who failed chloroquine therapy.
PfW2 can be obtained from the European Malaria Reagent Repository or the Malaria Research and Reference Reagent Resource Center (MR4) and is reported to be resistant to chloroquine and susceptible to mefloquine.
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 Ring formation assay (48 hours) - - <4.0 pIC50 - 1
⤷ pIC50 <4.0 (IC50 >1x10-4 M) FACS analysis following 48 hours in culture (second-generation rings) [1]
Lifecycle stages: Plasmodium asexual blood stage (erythrocytic merozoite, trophozoite, erythrocytic schizont)