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BY13   Click here for help

GtoPdb Ligand ID: 13933

Compound class: Synthetic organic
Comment: BY13 is designed to degrade the oncogene nuclear receptor coactivator 3 protein (NCOA3; also known as steroid receptor coactivator 3 or SRC3) [1]. It is a PROTAC class degrader, that binds the protein and recruits it to the cereblon E3 ubiquitin proteasome system for degradation. BY13 effectively blocks signalling downstream of the estrogen receptor (ER).
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 13
Hydrogen bond donors 2
Rotatable bonds 7
Topological polar surface area 142.38
Molecular weight 645.71
XLogP 1.87
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 C/C(=N\NC1=NC2=C(C=CC=C2)N1C3CN(C3)C4CCN(CC4)C5=C6C(=CC=C5)C(=O)N(C7CCC(=O)NC7=O)C6=O)/C8=NC=CC=C8
Isomeric SMILES C/C(/C1=CC=CC=N1)=N\NC2=NC3=CC=CC=C3N2C4CN(C5CCN(C6=CC=CC=7C(N(C8CCC(NC8=O)=O)C(C76)=O)=O)CC5)C4
InChI InChI=1S/C35H35N9O4/c1-21(25-8-4-5-16-36-25)39-40-35-37-26-9-2-3-10-27(26)43(35)23-19-42(20-23)22-14-17-41(18-15-22)28-11-6-7-24-31(28)34(48)44(33(24)47)29-12-13-30(45)38-32(29)46/h2-11,16,22-23,29H,12-15,17-20H2,1H3,(H,37,40)(H,38,45,46)/b39-21+
InChI Key AXNQNPVSVCEGTP-LALXJTNGSA-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/)
References
1. Liang J, Wang D, Wu Y, Shi J, Xie B, Xiao R, Ni J, Wang C, Dong C, Shu HB et al.. (2025)
Intercepting the Downstream of the Estrogen Receptor Signaling Pathway: Discovery of a Potent and Efficient SRC-3 PROTAC Degrader for Overcoming Endocrine Resistance Breast Cancer.
J Med Chem, [Epub ahead of print]. [PMID:40434408]