compound 13 [Chen et al., 2016]   Click here for help

GtoPdb Ligand ID: 9205

Compound class: Synthetic organic
Comment: Compound 13 is reported as a DOT1L inhibitor, with a novel chemical structure, distinct from that of pinometostat (EPZ-5676) [1]. Compound 13 acts as a SAM-competitive inhibitor, binding to an induced pocket adjacent to the SAM binding site.
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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 2
Rotatable bonds 6
Topological polar surface area 94.19
Molecular weight 476.21
XLogP 4.86
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 CNc1ccnc(n1)Nc1ccc2c(c1)n(c(c2)C)c1ccccc1Oc1cnc2c(c1)ncn2C
Isomeric SMILES CNc1ccnc(n1)Nc1ccc2c(c1)n(c(c2)C)c1ccccc1Oc1cnc2c(c1)ncn2C
InChI InChI=1S/C27H24N8O/c1-17-12-18-8-9-19(32-27-29-11-10-25(28-2)33-27)13-23(18)35(17)22-6-4-5-7-24(22)36-20-14-21-26(30-15-20)34(3)16-31-21/h4-16H,1-3H3,(H2,28,29,32,33)
InChI Key RQVLGMREYUFLPQ-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
Compound 13 exhibits a favourable selectivity profile against a panel of 22 PKMTs and PRMTs with no inhibitory activity up to 50μM [1]. It also suppress H3K79 dimethylation (IC50 16nM) and has a long on-target residence time as assessed by surface plasmon resonance experiments (> 240 minutes). In vitro, compound 13 effectively inhibits proliferation of the human MLL-rearranged leukemia cell line MV4-11 which expresses the oncogenic MLL-AF4 fusion .
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
DOT1 like histone lysine methyltransferase Hs Inhibitor Inhibition 10.1 pKi - 1
⤷ pKi 10.1 (Ki 8x10-11 M) [1]
Description: Scintillation proximity assay result