YX862   Click here for help

GtoPdb Ligand ID: 13483

Synonyms: compound 38 [PMID: 38949959] | YX-862
Compound class: Synthetic organic
Comment: YX862 ia a PROTAC degrader of histone deacetylase 8 (HDAC8) [1]. It is a von Hippel-Lindau (VHL)-recruiting PROTAC with a hydrazide warhead to engage the target and it was designed as a potential antitumour agent.
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 13
Hydrogen bond donors 5
Rotatable bonds 27
Topological polar surface area 184.01
Molecular weight 873.2
XLogP 6.08
No. Lipinski's rules broken 4

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 CCCCCCNNC(=O)C1=CC=C(C=C1)N2CCN(CCCCCCCC(=O)N[C@H](C(=O)N3C[C@@H](C[C@H]3C(=O)N[C@@H](C)C4=CC=C(C=C4)C5=C(C)N=CS5)O)C(C)(C)C)CC2
Isomeric SMILES O=C(N1[C@H](C(N[C@@H](C)C2=CC=C(C3=C(C)N=CS3)C=C2)=O)C[C@@H](O)C1)[C@H](C(C)(C)C)NC(CCCCCCCN4CCN(CC4)C5=CC=C(C(NNCCCCCC)=O)C=C5)=O
InChI InChI=1S/C48H72N8O5S/c1-7-8-9-14-25-50-53-45(59)38-21-23-39(24-22-38)55-29-27-54(28-30-55)26-15-12-10-11-13-16-42(58)52-44(48(4,5)6)47(61)56-32-40(57)31-41(56)46(60)51-34(2)36-17-19-37(20-18-36)43-35(3)49-33-62-43/h17-24,33-34,40-41,44,50,57H,7-16,25-32H2,1-6H3,(H,51,60)(H,52,58)(H,53,59)/t34-,40+,41-,44+/m0/s1
InChI Key ZOSWUNAJRAEGEW-YTIGDUPRSA-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 YX862 in vitro is 2.6 nM, and it achieves >95% degradation [1]. YX862 mediates an HDAC8-specific antiproliferative effect in tumour cells in vitro.