M4205   Click here for help

GtoPdb Ligand ID: 11510

Synonyms: compound 32 [PMID: 36728508] | IDRX-42 [1] | IDRX42 | M-4205
PDB Ligand
Compound class: Synthetic organic
Comment: M4205 is a potent and selective inhibitor of the KIT proto-oncogene, receptor tyrosine kinase (cKIT). It retains activity against cKIT with exon 11, 13 or 17 resistance mutations, and provides good selectivity in biochemical and cellular assays. M4205's ADME profile supports its potential as an orally bioavailable clinical candidate [1].
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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 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 6
Hydrogen bond donors 1
Rotatable bonds 10
Topological polar surface area 85.4
Molecular weight 508.27
XLogP 4.58
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 Cn1ncc(c1)c1ccc(cc1)CNc1ncnc(c1)c1cnc2n1ccc(c2)OCCCN1CCCC1
Isomeric SMILES Cn1ncc(c1)c1ccc(cc1)CNc1ncnc(c1)c1cnc2n1ccc(c2)OCCCN1CCCC1
InChI InChI=1S/C29H32N8O/c1-35-20-24(18-34-35)23-7-5-22(6-8-23)17-30-28-16-26(32-21-33-28)27-19-31-29-15-25(9-13-37(27)29)38-14-4-12-36-10-2-3-11-36/h5-9,13,15-16,18-21H,2-4,10-12,14,17H2,1H3,(H,30,32,33)
InChI Key LVMAULGVWBINFP-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/)
Bioactivity Comments
M4205 inhibits cKITV654A with IC50 10 nM, and it achieves 65% inhibition of wild type cKIT activity in vitro. It is not a very selective inhibitor, as it has nanomolar potency (in a biochemical screening assay) at all of the Type III receptor tyrosine kinases [1]. In this assay system, M4205 exhibited slightly improved selectivity in comparison to the approved KIT inhibitors sunitinib, regorafenib, and ripretinib.
Selectivity at catalytic receptors
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
platelet derived growth factor receptor beta Hs Inhibitor Inhibition 8.6 pIC50 - 1
⤷ pIC50 8.6 (IC50 2.6x10-9 M) [1]
Description: Biochemical inhibitory potency
colony stimulating factor 1 receptor Hs Inhibitor Inhibition 8.3 pIC50 - 1
⤷ pIC50 8.3 (IC50 5.5x10-9 M) [1]
Description: Biochemical inhibitory potency
KIT proto-oncogene, receptor tyrosine kinase Hs Inhibitor Inhibition 7.4 pIC50 - 1
⤷ pIC50 7.4 (IC50 4.4x10-8 M) [1]
platelet derived growth factor receptor alpha Hs Inhibitor Inhibition 7.3 pIC50 - 1
⤷ pIC50 7.3 (IC50 5x10-8 M) [1]
Description: Biochemical inhibitory potency