LLC0424   Click here for help

GtoPdb Ligand ID: 13380

Synonyms: compound 10l [PMID: 38687638] | LLC-0424
Compound class: Synthetic organic
Comment: LLC0424 is a PROTAC degrader of the histone methyltransferase and oncology therapeutic target, nuclear receptor binding SET domain protein 2 (NSD2) [2]. The parental NSD2 targeting ligand (UNC6934) of the PROTAC binds to the protein's PWWP1 (chromatin binding) domain (Kd 91 nM) [1]. The cereblon E3 ligase is recruited by a thalidomide moiety.

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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 16
Hydrogen bond donors 4
Rotatable bonds 13
Topological polar surface area 203.63
Molecular weight 823.85
XLogP -0.23
No. Lipinski's rules broken 2

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 C1=C(C=CC(=C1)C(=O)NC2=CC=C(C=C2)C(=O)NC3CCN(CC3)C4=CC=C5C(=C4)C(=O)N(C6CCC(=O)NC6=O)C5=O)CN(C7CC7)C(=O)C8=CC=C9C(=C8)OCC(=O)N9
Isomeric SMILES C1(CC1)N(C(=O)C=2C=CC3=C(OCC(N3)=O)C2)CC4=CC=C(C=C4)C(NC5=CC=C(C=C5)C(NC6CCN(CC6)C=7C=C8C(N(C(C8=CC7)=O)C9C(NC(CC9)=O)=O)=O)=O)=O
InChI InChI=1S/C45H41N7O9/c53-38-16-15-36(42(57)49-38)52-44(59)33-13-12-32(22-34(33)45(52)60)50-19-17-30(18-20-50)47-41(56)27-5-8-29(9-6-27)46-40(55)26-3-1-25(2-4-26)23-51(31-10-11-31)43(58)28-7-14-35-37(21-28)61-24-39(54)48-35/h1-9,12-14,21-22,30-31,36H,10-11,15-20,23-24H2,(H,46,55)(H,47,56)(H,48,54)(H,49,53,57)
InChI Key OHRABUZLZFHHEJ-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
LLC0424-mediated selective NSD2 protein degradation has been demonstrated in in vitro and in vivo models [2]. The in vitro DC50 value is 20 nM (Dmax 96%) in acute lymphoblastic leukemia (ALL) RPMI-8402 cells (which express a gain-of-function NSD2 mutation).
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
nuclear receptor binding SET domain protein 2 Hs None Binding - - - 2
⤷ PROTAC [2]