PROTAC D16-M1P2
PROTAC D16-M1P2 is an orally active CRBN-mediated selective PKMYT1 PROTAC degrader, with a DC50 of 0.7 nM in CCNE1-amplified HCC1569 breast cancer cells. PROTAC D16-M1P2 induces PKMYT1 degradation via the ubiquitin-proteasome system, directly inhibits PKMYT1 kinase activity, suppresses Thr14 phosphorylation of CDK1, and depends on functional CRBN and ubiquitination-like modification processes. PROTAC D16-M1P2 can be used for the research of CCNE1-amplified breast cancer, FBXW7-mutated cholangiocarcinoma, and PPP2R1A-deficient cancers.
(Pink: PKMYT1 ligand (HY-180484); Blue: Cereblon E3 ligase ligand; Black: linker).
For research use only. We do not sell to patients.
- Purity : 99.94%
- Formula: C43H45FN10O4
- Molecular Weight:784.88
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Storage:Powder -20°C, 3 years , 4°C, 2 years ; In solvent -80°C, 6 months , -20°C, 1 month
To place orders, for customer services and technical support, please contact: MedChemExpress USA
Tel: 609-228-6898 E-mail: [email protected] [email protected]
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Biological Activity
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Chemical Information
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Solvent & Solubility
- Protocols
- Purity & Documentation
- References
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Help & FAQs
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Biological Activity
Description
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PKMYT1 0.7 nM (DC50) |
PKMYT1 7.6 nM (IC50) |
CDK1 |
In Vitro
PROTAC D16-M1P2 (100 μM (3-fold serial dilutions, 10 gradients); 15 min (compound + PKMYT1); 60 min (tracer addition); 60 min (GST-Tb addition)) potently binds purified recombinant human PKMYT1 with an IC50 range of 4.1-5.0 nM in a competitive HTRF binding assay[1].
PROTAC D16-M1P2 inhibits purified recombinant human PKMYT1 enzymatic activity with an IC50 of 7.6 nM in an ADP-Glo kinase assay[1].
PROTAC D16-M1P2 (10 min (compound + kinase); 60 min (kinase reaction with substrate and ATP)) shows over 50-fold selectivity for purified recombinant human PKMYT1 over BRAF, RAF1, and SRC, with IC50 values of 485.3 nM, 373.1 nM, and 398.5 nM respectively[1].
PROTAC D16-M1P2 (30 min (compound + cells); 2 h (tracer addition)) engages intracellular PKMYT1 in transiently transfected HEK293 cells with an EC50 of 12.0 nM in a NanoBRET assay[1].
PROTAC D16-M1P2 (1 µs) (in both R- and S-oxa-azaspirodecane linker configurations) selectively accommodates the PKMYT1-CRBN-M4 conformation, forming moderately stable ternary complexes with docking scores of -10.85 kcal/mol (R) and -10.70 kcal/mol (S) that maintain sustained ubiquitination accessibility over 1 µs MD simulations[3].
PROTAC D16-M1P2 (100 ns) has linker length distributions compatible with the productive PKMYT1-CRBN-M4 conformation, consistent with its potent PKMYT1 degradation activity (DC50 = 0.70 nM)[3].
PROTAC D16-M1P2 (0.01-1000 nM; 24 h) induces potent, dose-dependent PKMYT1 degradation (DC50 0.7 nM, Dmax 90%) and pCDK1 (Thr14) inhibition (IC50 9.0 nM) in CCNE1-amplified HCC1569 breast cancer cells after 24 h treatment[1].
PROTAC D16-M1P2 (1 nM; 100 nM; 2, 4, 8, 24 h) induces rapid, time-dependent PKMYT1 degradation and pCDK1(Thr14) inhibition in CCNE1-amplified HCC1569 breast cancer cells, with 100 nM treatment producing robust pathway suppression while 1 nM treatment only induces partial degradation without significant signaling inhibition[1].
PROTAC D16-M1P2 (100 nM; 24 h pretreatment; 0, 2, 4, 16, 24 h post-washout incubation) induces durable PKMYT1 degradation and pCDK1Thr14 inhibition in CCNE1-amplified HCC1569 breast cancer cells, with effects sustained for at least 24 h after compound washout[1].
PROTAC D16-M1P2 (0.1 μM; 24 h) mediates PKMYT1 degradation in CCNE1-amplified HCC1569 breast cancer cells via a ubiquitin-proteasome system-dependent mechanism requiring both PKMYT1 and CRBN binding[1].
PROTAC D16-M1P2 (10 nM; 100 nM; 8 h) exhibits high proteome-wide selectivity for PKMYT1 in CCNE1-amplified HCC1569 breast cancer cells, with PKMYT1 being the only significantly degraded protein after 8 h treatment at 10 nM or 100 nM[1].
PROTAC D16-M1P2 (7 days) inhibits proliferation of human tumor cell lines with CCNE1 amplification, FBXW7 mutation, or PPP2R1A loss with 12-fold selectivity over wild-type cell lines, with an average IC50 of 177 nM in biomarker-positive cells after 7 days of treatment[1].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only. Further protocols information, click here.
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Cell Line:HCC1569 breast cancer cells (CCNE1-amplified)
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Concentration:0.02-1000 nM
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Incubation Time:24 h
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Result:Induced dose-dependent PKMYT1 degradation with a DC50 of 0.7 nM and a maximum degradation (Dmax) of 90%.
Inhibited pCDK1 (Thr14) with an IC50 of 9.0 nM, superior to other D16 diastereoisomers.
Showed a hook effect at concentrations above maximal degradation, where PKMYT1 degradation decreased but pCDK1 inhibition continued to increase.
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Cell Line:HCC1569 breast cancer cells (CCNE1-amplified)
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Concentration:1 nM; 100 nM
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Incubation Time:2, 4, 8, 24 h
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Result:At 100 nM, reduced PKMYT1 levels by over 80% within 4 h and reached maximal degradation at 24 h (faster than PKMYT1's natural half-life of 12.5 h).
At 100 nM, achieved over 50% pCDK1 (Thr14) inhibition after 4 h, sustained for at least 24 h.
At 1 nM, induced ~60% PKMYT1 degradation after 8-24 h but did not produce significant pCDK1 (Thr14) inhibition.
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Cell Line:HCC1569 breast cancer cells (CCNE1-amplified)
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Concentration:0.1 μM D16-M1P2; 0.3, 1 μM MLN-4924; 0.1, 1 μM MG-132; 3, 10 μM pomalidomide; 0.1 μM compound 4
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Incubation Time:24 h
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Result:PKMYT1 degradation induced by D16-M1P2 was completely abolished in the presence of MG-132, MLN-4924, pomalidomide, or compound 4.
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Cell Line:HCC1569 breast cancer cells (CCNE1-amplified)
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Concentration:100 nM
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Incubation Time:24 h pretreatment; 0, 2, 4, 16, 24 h post-washout incubation
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Result:PKMYT1 degradation and pCDK1 (Thr14) inhibition were maintained for at least 24 h post-washout.
Showed sustained effects in contrast to reference inhibitor RP-6306 whose inhibitory effect reversed within 2 h.
Parmacokinetics
| Species | Dose | Route | CLplasma | Vdss | T1/2 | Cmax | AUClast | Bioavailability |
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| Mice[1] | 1 mg/kg | i.v. | 80.2 mL/min/kg | 6.6 L/kg | / | / | / | / |
| Mice[1] | 40 mg/kg | p.o. | / | / | 3.2 h | 1181 ng/mL | 7436 ng·h/mL | 91.3 % |
| Rat[1] | 1 mg/kg | i.v. | 17.6 mL/min/kg | 3.7 L/kg | / | / | / | / |
| Rat[1] | 20 mg/kg | p.o. | / | / | 7.7 h | 2269 ng/mL | 29851 ng·h/mL | 166.5 % |
| Dog[1] | 1 mg/kg | i.v. | 7.2 mL/min/kg | 3.3 L/kg | / | / | / | / |
| Dog[1] | 5 mg/kg | p.o. | / | / | 6.3 h | 583 ng/mL | 7461 ng·h/mL | 67.9 % |
| Monkey[1] | 1 mg/kg | i.v. | 19.3 mL/min/kg | 5.1 L/kg | / | / | / | / |
| Monkey[1] | 10 mg/kg | p.o. | / | / | 10.9 h | 144 ng/mL | 1721 ng·h/mL | 20.5 % |
In Vivo
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
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Animal Model:NOD.CB17-Prkdcscid/NcrCrl (female, 6-8 weeks old, ~23-26 g)[1]
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Dosage:40 mg/kg; 120 mg/kg
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Administration:p.o.; twice daily; 21 days
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Result:Achieved 35.1% tumor growth inhibition (TGI) at 40 mg/kg.
Achieved 66.4% TGI at 120 mg/kg.
Induced ~65% PKMYT1 degradation and ~45% inhibition of pCDK1 (T14) at 8 hours post-last 40 mg/kg dose.
Induced ~75% PKMYT1 degradation and ~70% inhibition of pCDK1 (T14) at 8 hours post-last 120 mg/kg dose.
Induced ~55% PKMYT1 degradation and ~30% inhibition of pCDK1 (T14) at 24 hours post-last 40 mg/kg dose.
Induced ~70% PKMYT1 degradation and ~55% inhibition of pCDK1 (T14) at 24 hours post-last 120 mg/kg dose.
Observed a significant positive correlation (r = 0.82, p = 0.001) between PKMYT1 degradation and pCDK1 (T14) inhibition.
Chemical Information
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Appearance Solid
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Molecular Weight 784.88
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Formula C43H45FN10O4
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Color Light yellow to yellow
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SMILES
N#CC1=[C@]([C@](C(C)=C(C=C2)O)=C2C)C=NC3=C1C=C(N3)C4=CN=C(N5CCC6(CC(N7CCN(C8=C(F)C=C(NC9CCC(NC9=O)=O)C=C8)CC7)CO6)CC5)N=C4
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month
Solvent & Solubility
In Vitro:
DMSO : 100 mg/mL (127.41 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
Protocols
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Kinase activity and phosphorylation assays
Kinase activity assays measure the ability of kinases to transfer phosphate groups from ATP to specific substrates, while phosphorylation assays detect the presence and levels of phosphorylated proteins. Common methods include radiolabeled ATP incorporation (e. g. ,), ADP release detection via bioluminescence (e. g. ,[3]), enzyme-linked immunosorbent assays (ELISA) for phospho-specific epitopes (e. g. ,[6]), and microtiter-based formats for high-throughput screening (e. g. ,[8]). The ADP-Glo assay quantifies kinase activity by measuring ADP produced during phosphorylation using a luciferase-based system. Radiometric assays involve autoradiography or scintillation counting after incorporation of 32P-labeled ATP into substrate proteins. ELISA-based approaches rely on phospho-specific antibodies to detect activated kinases in cell lysates or purified samples.
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Western Blot
Western blotting (WB) is a commonly used experimental method in molecular biology, biochemistry, and immunogenetics for identifying and quantifying target proteins. It combines gel electrophoresis with immunoassay, enabling researchers to analyze protein expression, post-translational modifications, and molecular weight.
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Protocol for Kinase activity and phosphorylation assays
Kinase activity assays measure transfer of phosphate from ATP to a protein or peptide substrate, generating phosphorylated substrate, ADP, or incorporated radiolabeled phosphate as the readout; phosphorylation assays measure site-specific phosphorylation in cells or tissues as a proxy for kinase-pathway activation, inhibition, or substrate regulation. Phosphorylation can be detected by phospho-specific Western blot, immunoprecipitation kinase assay, phospho-immunofluorescence, phospho-flow cytometry, luminescent ADP detection, radiolabeled ATP incorporation, or reporter-based pathway assays, and these readouts can be applied to cancer cells, primary neurons, mouse tumors, organoids, inflammatory macrophages, ferroptosis studies, and mitophagy studies when the kinase target is biologically relevant.
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Breast Cancer Modeling
Breast cancer is a heterogeneous cancer, and it has been distinguished into four subtypes: luminal A, luminal B, HER2-positive and basal-like. Molecular mutations, epigenetic alterations, hormone exposure and immune microenvironment are related to the progression of breast cancer.
Purity & Documentation
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Data Sheet (283 KB)
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SDS (252 KB)
- English - EN (252 KB)
- Français - FR (252 KB)
- Deutsch - DE (252 KB)
- Norwegian - NO (252 KB)
- Español - ES (252 KB)
- Swedish - SV (252 KB)
- Italian - IT (252 KB)
- Korean - KR (252 KB)
- Portuguese - PT (252 KB)
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Handling Instructions (2659 KB)
References
[1]. Wang Y, et al. Discovery of a bifunctional PKMYT1-targeting PROTAC empowered by AI-generation. Nature communications. 2025 Nov 28;16(1):10759. [Content Brief]
[2]. Li L, et al. PKMYT1 in Cancer: Beyond Cell Cycle Checkpoints to Context-Dependent Therapeutic Vulnerability. Genes, chromosomes & cancer. 2026 Jul;65(7):e70151. [Content Brief]
[3]. Nassar H, et al. Computational mapping of productive POI-E3 ligase conformations to guide de novo degrader design: application to WEE1 and PKMYT1 PROTACs. Journal of cheminformatics. 2026 Jul 24;18(1):103. [Content Brief]
Complete Stock Solution Preparation Table
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
| Optional Solvent | Concentration Solvent Mass | 1 mg | 5 mg | 10 mg | 25 mg |
|---|---|---|---|---|---|
| DMSO | 1 mM | 1.2741 mL | 6.3704 mL | 12.7408 mL | 31.8520 mL |
| 5 mM | 0.2548 mL | 1.2741 mL | 2.5482 mL | 6.3704 mL | |
| 10 mM | 0.1274 mL | 0.6370 mL | 1.2741 mL | 3.1852 mL | |
| 15 mM | 0.0849 mL | 0.4247 mL | 0.8494 mL | 2.1235 mL | |
| 20 mM | 0.0637 mL | 0.3185 mL | 0.6370 mL | 1.5926 mL | |
| 25 mM | 0.0510 mL | 0.2548 mL | 0.5096 mL | 1.2741 mL | |
| 30 mM | 0.0425 mL | 0.2123 mL | 0.4247 mL | 1.0617 mL | |
| 40 mM | 0.0319 mL | 0.1593 mL | 0.3185 mL | 0.7963 mL | |
| 50 mM | 0.0255 mL | 0.1274 mL | 0.2548 mL | 0.6370 mL | |
| 60 mM | 0.0212 mL | 0.1062 mL | 0.2123 mL | 0.5309 mL | |
| 80 mM | 0.0159 mL | 0.0796 mL | 0.1593 mL | 0.3982 mL | |
| 100 mM | 0.0127 mL | 0.0637 mL | 0.1274 mL | 0.3185 mL |
PROTAC D16-M1P2 Related Classifications
HY-180485 Related Classifications
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