YTHDC1 inhibitor 40   Click here for help

GtoPdb Ligand ID: 13394

PDB Ligand
Compound class: Synthetic organic
Comment: This is a selective small molecule inhibitor of the m6A reader function of the YTHDC1 protein [1]. The crystal structure of the YTHDC1-inhibitor 40 complex has been resolved (PDB ID 8Q4W).
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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

YTHDC1 inhibitor 40 is commercially available from our sponsors

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 5
Hydrogen bond donors 2
Rotatable bonds 3
Topological polar surface area 61.14
Molecular weight 308.17
XLogP 2.04
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 CNC1=C2C(=NC(=N1)Cl)C(=NN2)CC3=CC=CC(=C3)Cl
Isomeric SMILES ClC1=NC=2C(CC3=CC(Cl)=CC=C3)=NNC2C(NC)=N1
InChI InChI=1S/C13H11Cl2N5/c1-16-12-11-10(17-13(15)18-12)9(19-20-11)6-7-3-2-4-8(14)5-7/h2-5H,6H2,1H3,(H,19,20)(H,16,17,18)
InChI Key ULSNLRVQBCXMSH-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
Inhibitor 40 is selective for YTHDC1 compared to the other human m6A reader proteins YTHDC2 and YTHDF1-3 [1]. It has antiproliferative activity against acute myeloid leukemia (AML) cell lines in vitro.
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
YTH N6-methyladenosine RNA binding protein C1 Hs Inhibitor Binding 7.3 pKd - 1
⤷ pKd 7.3 (Kd 4.9x10-8 M) [1]
Description: Equilibrium dissociation constant