GtoPdb is requesting financial support from commercial users. Please see our sustainability page for more information.

CDK2 PROTAC 37   Click here for help

GtoPdb Ligand ID: 14477

Compound class: Synthetic organic
Comment: This is an orally bioavailable, heterobifunctional PROTAC class degrader of the cyclin dependent kinase 2 (CDK2) protein [1]. CDK2 binding is mediated by a PF-06873600-derived moiety. This PROTAC mediates formation of a CDK2/Cyclin E1-cereblon (CRBN E3 ligase) ternary complex that is directed for proteasomal degradation. The PROTAC approach is proposed to act on CDK2-dependent tumours (e.g. with CCNE1 gene defects), and tumours with acquired resistance to CDK4/6 inhibitor therapies.
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 4
Rotatable bonds 11
Topological polar surface area 167.42
Molecular weight 852.89
XLogP 2.09
No. Lipinski's rules broken 3

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 C[C@@]1(CCCN(C1)C2=C(C=NC(=N2)NC3=CC=C(C=C3F)S(=O)(=O)N[C@@H]4CCN(CC5CCN(CC5)C6=CC=C(C=C6F)C7CCC(=O)NC7=O)C[C@@H]4F)C(F)(F)F)O
Isomeric SMILES C1(C2=CC(F)=C(N3CCC(CN4CC[C@@H](NS(C5=CC=C(NC6=NC=C(C(F)(F)F)C(N7CCC[C@](C)(O)C7)=N6)C(F)=C5)(=O)=O)[C@@H](F)C4)CC3)C=C2)CCC(=O)NC1=O
InChI InChI=1S/C39H46F6N8O5S/c1-38(56)12-2-13-53(22-38)35-27(39(43,44)45)19-46-37(49-35)47-31-6-4-25(18-28(31)40)59(57,58)50-32-11-14-51(21-30(32)42)20-23-9-15-52(16-10-23)33-7-3-24(17-29(33)41)26-5-8-34(54)48-36(26)55/h3-4,6-7,17-19,23,26,30,32,50,56H,2,5,8-16,20-22H2,1H3,(H,46,47,49)(H,48,54,55)/t26?,30-,32+,38-/m0/s1
InChI Key MQWDHROLFNTJMK-PONYFJNFSA-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. Collier PN, Zheng X, Ford M, Weiss M, Chen D, Li K, Growney JD, Yang A, Sathappa M, Breitkopf SB et al.. (2025)
Discovery of Selective and Orally Bioavailable Heterobifunctional Degraders of Cyclin-Dependent Kinase 2.
J Med Chem, 68 (17): 18407-18422. [PMID:40833690]