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compound 3 [PMID: 32258933]   Click here for help

GtoPdb Ligand ID: 11214

Antimalarial Ligand
Compound class: Synthetic organic
Comment: Compound 3 is the lead for a novel series of antimalarial compounds based on a benzimidazole core [1].

The Malaria tab on this ligand page provides additional curator comments of relevance to the Guide to MALARIA PHARMACOLOGY.
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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Click here for structure editor
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 3
Hydrogen bond donors 1
Rotatable bonds 3
Topological polar surface area 33.09
Molecular weight 326.13
XLogP 4.18
No. Lipinski's rules broken 0

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 Clc1ccc2c(c1)nc(n2Cc1ccccc1)N1CCNCC1
Isomeric SMILES Clc1ccc2c(c1)nc(n2Cc1ccccc1)N1CCNCC1
InChI InChI=1S/C18H19ClN4/c19-15-6-7-17-16(12-15)21-18(22-10-8-20-9-11-22)23(17)13-14-4-2-1-3-5-14/h1-7,12,20H,8-11,13H2
InChI Key RDAXAGXJSCEYLT-UHFFFAOYSA-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/)
Classification Click here for help
Compound class Synthetic organic
Ligand families/groups Antimalarial ligands
IUPAC Name Click here for help
5-chloro-1-(phenylmethyl)-2-piperazin-1-ylbenzimidazole
Database Links Click here for help
ChEMBL Ligand CHEMBL294083
GtoPdb PubChem SID 434122274
PubChem CID 10806082
Search Google for chemical match using the InChIKey RDAXAGXJSCEYLT-UHFFFAOYSA-N
Search Google for chemicals with the same backbone RDAXAGXJSCEYLT
UniChem Compound Search for chemical match using the InChIKey RDAXAGXJSCEYLT-UHFFFAOYSA-N
UniChem Connectivity Search for chemical match using the InChIKey RDAXAGXJSCEYLT-UHFFFAOYSA-N