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
No information available.
Summary of Clinical Use Click here for help
Clindamycin is used to treat a wide range of bacterial infections. These include bone and joint infections, gynaecological infections, intra-abdominal infections, lower respiratory infections, septicemia and skin infections. A combined therapy of clindamycin with fosmidomycin to treat uncomplicated P. falciparum malaria shows promising results, progressing to Phase 3 (NCT00214643). It is also used to treat uncomplicated malaria (particularly useful in areas where chloroquine or multidrug-resistant strains of P. falciparum are found) and as an effective treatment for severe malaria, when used as a combination therapy [6]. It should not be used as a monotherapy for malaria treatment due to a delayed antimalarial effect (see MOA for more details).
Mechanism Of Action and Pharmacodynamic Effects Click here for help
Antibacterial MMOA is reversible binding to the 50S ribosomal subunits to prevent peptide-bond formation by sterically blocking A-site tRNA positioning at the peptidyl-transferase centre (PTC) and thereby inhibiting bacterial protein synthesis [2]. In Plasmodium, pharmacological concentrations of the compound kill the parasite in the lifecycle after treatment starts. It is thought that clindamycin inhibits the production of proteins encoded by the apicoplast genome, leading to a subsequent loss of apicoplast function and a possible explanation for the delayed antimalarial effect [1].
Clinical Trials
Clinical Trial ID Title Type Source Comment References
NCT00214643 Efficacy of Fosmidomycin-Clindamycin for Treating Malaria in Gabonese Children Phase 3 Interventional Albert Schweitzer Hospital
External links Click here for help
For extended ADME data see the following:

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