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DNMT1 degrader 6k   Click here for help

GtoPdb Ligand ID: 14453

Compound class: Synthetic organic
Comment: Compound 6k is reported as a DNA methyltransferase 1 (DNMT1) molecular glue type degrader [1]. It binds at the interface between DNMT1 and the RING-finger type E3 ubiquitin ligase UHRF1, and enhances the binding affinity between the protein pair from >2 μM in the absence of 6k to 24 nM in its presence. Compound 6k promotes UHRF1-mediated degradation of DNMT1.
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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 6
Hydrogen bond donors 0
Rotatable bonds 5
Topological polar surface area 49.66
Molecular weight 408.54
XLogP 3.14
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=CC2=C(N=C(C3=CCCC3)N=C2C=C1OC)N4CCC(CC4)N5CCCC5
Isomeric SMILES COC1=C(OC)C=C2C(C(N3CCC(N4CCCC4)CC3)=NC(C5=CCCC5)=N2)=C1
InChI InChI=1S/C24H32N4O2/c1-29-21-15-19-20(16-22(21)30-2)25-23(17-7-3-4-8-17)26-24(19)28-13-9-18(10-14-28)27-11-5-6-12-27/h7,15-16,18H,3-6,8-14H2,1-2H3
InChI Key DIDDMGZNRDOWDK-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/)

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