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ZN-c5   Click here for help

GtoPdb Ligand ID: 13967

Synonyms: compound F [WO2021216671A1] | example 5A [US20210330651A1] | ZNc5
Compound class: Synthetic organic
Comment: ZN-c5 was developed as an orally bioavailable selective estrogen receptor degrader (SERD) [1], for potential to treat breast cancer brain metastases. The core structure of ZN-c5 was used in the design of compounds with improved brain penetration and in vitro and in vivo efficacy, such as compound 5 [PMID: 40393772] [3].
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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Click here for structure editor
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 4
Hydrogen bond donors 2
Rotatable bonds 4
Topological polar surface area 52.57
Molecular weight 434.48
XLogP 2.72
No. Lipinski's rules broken 0

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@@H]1CC2=C([C@@H](C3=C(C=C(/C=C/C(=O)O)C=C3F)F)N1C45CC(C4)C5)NC6=C2C=CC=C6
Isomeric SMILES C[C@@H]1CC2=C([C@H](N1C34CC(C3)C4)C5=C(C=C(C=C5F)/C=C/C(=O)O)F)NC6=CC=CC=C26
InChI InChI=1S/C26H24F2N2O2/c1-14-8-18-17-4-2-3-5-21(17)29-24(18)25(30(14)26-11-16(12-26)13-26)23-19(27)9-15(10-20(23)28)6-7-22(31)32/h2-7,9-10,14,16,25,29H,8,11-13H2,1H3,(H,31,32)/b7-6+/t14-,16?,25-,26?/m1/s1
InChI Key HGFYTUMJTQXEII-JMAUQWQESA-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. Huang PQ, Hedge SG, Bunker KD, Knight J, Pinchman JR, Unni AK, Sit RK, Zhu S, Hopkins CD, Scott I. (2021)
Preparation of an selective estrogen receptor degrader.
Patent number: WO2021216671A1. Assignee: Recurium Ip Holdings, Llc. Priority date: 21/04/2021. Publication date: 28/10/2021.
2. Huang PQ, Slee DH, Hedge SG, Hopkins CD, Bunker KD, Pinchman JR, Sit RK. (2021)
Estrogen receptor modulators.
Patent number: US20210330651A1. Assignee: KALYRA PHARMACEUTICALS, INC.. Priority date: 06/07/2021. Publication date: 28/10/2021.
3. Zhang G, Huang PQ, Bunker KD, Hegde SG, Ma J, Lee CC, Samatar AA, Unni A, Al-Amin M, Kakarla R. (2025)
Discovery of an Orally Bioavailable and Brain Penetrant Selective Estrogen Receptor Degrader.
J Med Chem, 68 (11): 11990-12003. [PMID:40393772]