PRMT5 inhibitor D3   Click here for help

GtoPdb Ligand ID: 13678

Synonyms: compound D3 [PMID: 39722476]
Compound class: Synthetic organic
Comment: This small molecule behaves as a selective inhibitor of protein arginine methyltransferase 5 (PRMT5) [1]. Its structure was designed through scaffold-hopping and SAR based on the non-nucleoside ex-clinical lead inhibitor GSK3326595.
Click here for help

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.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

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.

✖
Hydrogen bond acceptors 8
Hydrogen bond donors 2
Rotatable bonds 7
Topological polar surface area 88.48
Molecular weight 515.65
XLogP -0.4
No. Lipinski's rules broken 1

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
Click here for help

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/)

✖
Canonical SMILES CC(=O)N1CC2(CC(C2)NC3=CC4=C(C=N3)C5(CC5)CN(C[C@@H](CN6CCC7=C(C=CC=C7)C6)O)C4=O)C1
Isomeric SMILES O=C1C2=CC(NC3CC4(CN(C(C)=O)C4)C3)=NC=C2C5(CC5)CN1C[C@H](O)CN6CCC7=C(C6)C=CC=C7
InChI InChI=1S/C30H37N5O3/c1-20(36)35-17-29(18-35)11-23(12-29)32-27-10-25-26(13-31-27)30(7-8-30)19-34(28(25)38)16-24(37)15-33-9-6-21-4-2-3-5-22(21)14-33/h2-5,10,13,23-24,37H,6-9,11-12,14-19H2,1H3,(H,31,32)/t24-/m1/s1
InChI Key PEYPSWDNEDTZFS-XMMPIXPASA-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
D3 has demonstrated anti-tumour activity in vitro and in vivo [1]. It induces cell cycle arrest and apoptosis in lymphoma models, and is selective for PRMT5 compared to other protein arginine N-methyltransferases.
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
protein arginine methyltransferase 5 Hs Inhibitor Inhibition 7.7 pIC50 - 1
⤷ pIC50 7.7 (IC50 2.07x10-8 M) [1]