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YD54   Click here for help

GtoPdb Ligand ID: 13901

Compound class: Synthetic organic
Comment: YD54 is an orally bioavailable, cereblon-engaging PROTAC degrader of SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 (SMARCA2) [3]. It is a bifunctional molecule containing a SMARCA2 bromodomain binding ligand linked to pomalidomide (to recruit the cereblon E3 ubiquitin ligase). Disrupting SMARCA2 is synthetic lethal in lung cancer cells that harbour loss of function mutations in the paralog SMARCA4 [1-2,4-5].
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 15
Hydrogen bond donors 3
Rotatable bonds 10
Topological polar surface area 176.71
Molecular weight 763.82
XLogP 1.58
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=CC(=C(C=C1)O)C2=NN=C(C(=C2)N3CCN(CC3)CC4=CC=C(C(=C4)F)N5CCN(CC5)CCOC6=C7C(=CC=C6)C(=O)N(C8CCC(=O)NC8=O)C7=O)N
Isomeric SMILES O=C1N(C2CCC(NC2=O)=O)C(=O)C3=C1C(=CC=C3)OCCN4CCN(C5=C(F)C=C(CN6CCN(C7=C(N)N=NC(C8=C(O)C=CC=C8)=C7)CC6)C=C5)CC4
InChI InChI=1S/C40H42FN9O6/c41-28-22-25(24-47-14-18-49(19-15-47)32-23-29(44-45-37(32)42)26-4-1-2-6-33(26)51)8-9-30(28)48-16-12-46(13-17-48)20-21-56-34-7-3-5-27-36(34)40(55)50(39(27)54)31-10-11-35(52)43-38(31)53/h1-9,22-23,31,51H,10-21,24H2,(H2,42,45)(H,43,52,53)
InChI Key WBWCGTJXNCHFJI-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
The DC50 for YD54 is in the low nanomolar range in various SMARCA4 mutant lung cancer cell lines [3]. YD54 selectively disrupts proliferation of SMARCA4 mutant cells, with little impact on the growth of cells with wild-type SMARCA4.
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 Hs None Binding - - - 3
⤷ PROTAC [3]