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RMC-113   Click here for help

GtoPdb Ligand ID: 14429

Compound class: Synthetic organic
Comment: RMC-113 is reported as an inhibitor of the lipid kinases PIP4K2C and PIKfyve [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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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 0
Rotatable bonds 3
Topological polar surface area 80.84
Molecular weight 373.43
XLogP 1.71
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 COC1=C(C=C(C=C1)C2=CC3=NSC(=C3N=C2)C#CC4=CC=CN=C4)OC
Isomeric SMILES COC1=C(C=C(C=C1)C2=CC3=NSC(=C3N=C2)C#CC4=CN=CC=C4)OC
InChI InChI=1S/C21H15N3O2S/c1-25-18-7-6-15(11-19(18)26-2)16-10-17-21(23-13-16)20(27-24-17)8-5-14-4-3-9-22-12-14/h3-4,6-7,9-13H,1-2H3
InChI Key XMKRMXXCWCKTSQ-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
RMC-113 suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids, likely through reversing autophagic flux impairment induced by PIP4K2C interaction with CoV nonstructural protein 6 (nsp6) [1]. In a cell-based kinome profiling analysis RMC-113 dose-dependently binds to PIKfyve, PIP4K2A, PIP4K2B, and PIP4K2C, but no/very low potency inhibition of kinase activity for PIP4K2A and PIP4K2B was detected in orthogonal kinase activity assays.
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
phosphatidylinositol-5-phosphate 4-kinase type 2 gamma Hs Inhibitor Binding 7.3 pKd - 1
⤷ pKd 7.3 (Kd 4.6x10-8 M) [1]
phosphoinositide kinase, FYVE-type zinc finger containing Hs Inhibitor Binding 6.4 pKd - 1
⤷ pKd 6.4 (Kd 3.7x10-7 M) [1]
phosphoinositide kinase, FYVE-type zinc finger containing Hs Inhibitor Inhibition 8.1 pIC50 - 1
⤷ pIC50 8.1 (IC50 8x10-9 M) [1]