primaquine   Click here for help

GtoPdb Ligand ID: 9952

Approved drug PDB Ligand Antimalarial Ligand
primaquine is an approved drug (FDA (1952))
Compound class: Synthetic organic
Comment: Primaquine is a synthetic, 8-aminoquinoline derivative that has potent antimalarial activity.
The approved drug is a racemic mixture and we show the chemical structure without stereochemistry to represent the mixture. The non-isomeric structure is also represented in the PubChem, ChEMBL and ChEBI entries listed in the links table below, while the two enantiomers forming the racemate are represented by PubChem CID 3044368 and PubChem CID 3044369.
The marketed formulations contain primaquine phosphate (PubChem CID 6135).

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 3
Hydrogen bond donors 2
Rotatable bonds 6
Topological polar surface area 60.17
Molecular weight 259.17
XLogP 2.09
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 NCCCC(Nc1cc(OC)cc2c1nccc2)C
Isomeric SMILES NCCCC(Nc1cc(OC)cc2c1nccc2)C
InChI InChI=1S/C15H21N3O/c1-11(5-3-7-16)18-14-10-13(19-2)9-12-6-4-8-17-15(12)14/h4,6,8-11,18H,3,5,7,16H2,1-2H3
InChI Key INDBQLZJXZLFIT-UHFFFAOYSA-N
Guide to Malaria Pharmacology Comments
Primaquine is effective against all exoerythrocytic forms of the malaria parasite, including the hypnozoite and is also active against the sexual blood stage (gametocytes). Primaquine was, until the approval of tafenoquine in 2018, the only licensed drug available for terminal prophylaxis to prevent relapse or delayed-onset clinical presentation of P. vivax and P. ovale malaria.
Primaquine is on the World Health Organisation's List of Essential Medicines. Click here to access the pdf version of the WHO's 21st Essential Medicines list (2019).

Potential Target/Mechanism Of Action: As the precise mechanism of action of primaquine is not yet known, we do not have a molecular target for this compound.