AZD5438

 CAS No.: 602306-29-6  Cat No.: BP-300176  Purity: 0.98 4.5  

AZD5438 is a CDK inhibitor-derived ligand that binds the ATP-binding region of CDK-family kinases and has been used as a target ligand for CDK2-directed PROTAC design. In a bifunctional degrader, the AZD5438-derived moiety provides CDK recognition, while a linker connects it to an E3 ligase recruiter to place the kinase near ubiquitination machinery. Productive ternary complex formation can induce CDK ubiquitination and proteasome-dependent depletion, enabling protein-level investigation of kinase function. This approach is valuable for distinguishing catalytic inhibition from selective degradation, especially in cellular models where CDK isoforms have overlapping but nonidentical functions. AZD5438 is useful for CDK2 degrader development, linker-geometry optimization, target engagement assays, cell-cycle pathway research, and comparative evaluation of CDK inhibitor scaffolds as PROTAC warheads.

AZD5438

Structure of 602306-29-6

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Ligand for Target Protein
Molecular Formula
C18H21N5O2S
Molecular Weight
371.45664
Appearance
White to off-white solid

* For research and manufacturing use only. Not for human or clinical use.

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Popular Publications Citing BOC Sciences Products
Purity
0.98
Appearance
White to off-white solid
IUPACName
4-(2-methyl-3-propan-2-ylimidazol-4-yl)-N-(4-methylsulfonylphenyl)pyrimidin-2-amine
Synonyms
AZD5438; AZD-5438; AZD 5438.
InChI Key
WJRRGYBTGDJBFX-UHFFFAOYSA-N
InChI
InChI=1S/C18H21N5O2S/c1-12(2)23-13(3)20-11-17(23)16-9-10-19-18(22-16)21-14-5-7-15(8-6-14)26(4,24)25/h5-12H,1-4H3,(H,19,21,22)
SMILES
CC1=NC=C(N1C(C)C)C2=NC(=NC=C2)NC3=CC=C(C=C3)S(=O)(=O)C
Mechanism

Target: This ligand targets cyclin-dependent kinases CDK1, CDK2, and CDK9 in biochemical or cellular target-engagement studies.

Mechanism of Action: Used as the target-protein recognition element, this ligand provides the binding interface for cyclin-dependent kinases CDK1, CDK2, and CDK9. In PROTAC design, a derivatizable position on the ligand can be connected through an optimized linker to an E3 ligase ligand, such as a CRBN, VHL, or IAP recruiter, while preserving productive target engagement. The resulting bifunctional molecule brings cyclin-dependent kinases CDK1 into proximity with the recruited E3 ligase, enabling ternary-complex formation. If the complex has favorable geometry and residence time, target lysine ubiquitination is promoted, leading to proteasome-dependent degradation in experimental systems.

Applications

• PROTAC-Mediated Degradation: AZD5438 can be used as a ligand component in PROTAC designs to recruit an E3 ligase and drive selective degradation of the corresponding target protein. By conjugating AZD5438 to an appropriate linker and E3-binding moiety, researchers can test degradation potency, kinetics, and dependence on ubiquitin–proteasome activity in cellular models.

• E3 Ligase Recruitment Optimization: In PROTAC research, AZD5438-based constructs enable systematic evaluation of different E3 ligase recruiters and linker lengths. This helps identify configurations that maximize ternary complex formation and promote efficient ubiquitination, thereby improving target knockdown beyond what is achievable with occupancy-based inhibitors.

• Ternary Complex Mechanism Studies: AZD5438 can support mechanistic studies of PROTAC action by enabling measurement of ternary complex stability between the target, PROTAC, and E3 ligase. Researchers can use biophysical and cellular assays to correlate complex formation with observed degradation, clarifying whether degradation is driven by productive engagement or rapid dissociation.

• Resistance and Specificity Profiling: AZD5438-containing PROTACs can be applied to investigate how target mutations, pathway rewiring, or altered E3 ligase expression affect degradation efficiency. Comparative profiling across related proteins can also assess specificity, helping refine ligand choice and PROTAC architecture to reduce off-target degradation.

• Proteostasis Pathway Validation: AZD5438-based PROTACs are suitable for validating downstream proteostasis effects, including accumulation of ubiquitinated substrates and dependence on proteasomal function. By combining degradation readouts with pathway perturbations, researchers can confirm that loss of the target protein results from targeted ubiquitin-mediated degradation rather than transcriptional or translational suppression.

1.Cyclin-dependent kinases regulate apoptosis of intestinal epithelial cells.
Bhattacharya S1, Ray RM, Johnson LR. Apoptosis. 2014 Mar;19(3):451-66. doi: 10.1007/s10495-013-0942-3.
Homeostasis of the gastrointestinal epithelium is dependent upon a balance between cell proliferation and apoptosis. Cyclin-dependent kinases (Cdks) are well known for their role in cell proliferation. Previous studies from our group have shown that polyamine-depletion of intestinal epithelial cells (IEC-6) decreases cyclin-dependent kinase 2 (Cdk2) activity, increases p53 and p21Cip1 protein levels, induces G1 arrest, and protects cells from camptothecin (CPT)-induced apoptosis. Although emerging evidence suggests that members of the Cdk family are involved in the regulation of apoptosis, their roles directing apoptosis of IEC-6 cells are not known. In this study, we report that inhibition of Cdk1, 2, and 9 (with the broad range Cdk inhibitor, AZD5438) in proliferating IEC-6 cells triggered DNA damage, activated p53 signaling, inhibited proliferation, and induced apoptosis. By contrast, inhibition of Cdk2 (with NU6140) increased p53 protein and activity, inhibited proliferation, but had no effect on apoptosis.
2.Development of cell-cycle inhibitors for cancer therapy.
Dickson MA1, Schwartz GK. Curr Oncol. 2009 Mar;16(2):36-43.
The cell cycle governs the transition from quiescence through cell growth to proliferation. The key parts of the cell cycle machinery are the cyclin-dependent kinases (CDKS) and the regulatory proteins called cyclins. The CDKS are rational targets for cancer therapy because their expression in cancer cells is often aberrant and their inhibition can induce cell death. Inhibitors of CDKS can also block transcription.Several drugs targeting the cell cycle have entered clinical trials. These agents include flavopiridol, indisulam, AZD5438, SNS-032, bryostatin-1, seliciclib, PD 0332991, and SCH 727965. Phase i studies have demonstrated that these drugs can generally be administered safely. Phase ii studies have shown little single-agent activity in solid tumors, but combination studies with cytotoxic chemotherapy have been more promising. In hematologic malignancies, reports have shown encouraging single-agent and combination activity. Pharmacodynamic studies show that the dose and schedule of these drugs are crucial to permit maximum therapeutic effect.
3.Selective pharmacologic inhibition of a PASTA kinase increases Listeria monocytogenes susceptibility to β-lactam antibiotics.
Pensinger DA1, Aliota MT2, Schaenzer AJ2, Boldon KM2, Ansari IU3, Vincent WJ1, Knight B1, Reniere ML4, Striker R5, Sauer JD6. Antimicrob Agents Chemother. 2014 Aug;58(8):4486-94. doi: 10.1128/AAC.02396-14. Epub 2014 May 27.
While β-lactam antibiotics are a critical part of the antimicrobial arsenal, they are frequently compromised by various resistance mechanisms, including changes in penicillin binding proteins of the bacterial cell wall. Genetic deletion of the penicillin binding protein and serine/threonine kinase-associated protein (PASTA) kinase in methicillin-resistant Staphylococcus aureus (MRSA) has been shown to restore β-lactam susceptibility. However, the mechanism remains unclear, and whether pharmacologic inhibition would have the same effect is unknown. In this study, we found that deletion or pharmacologic inhibition of the PASTA kinase in Listeria monocytogenes by the nonselective kinase inhibitor staurosporine results in enhanced susceptibility to both aminopenicillin and cephalosporin antibiotics. Resistance to vancomycin, another class of cell wall synthesis inhibitors, or antibiotics that inhibit protein synthesis was unaffected by staurosporine treatment.
4.AZD5438, a potent oral inhibitor of cyclin-dependent kinases 1, 2, and 9, leads to pharmacodynamic changes and potent antitumor effects in human tumor xenografts.
Byth KF1, Thomas A, Hughes G, Forder C, McGregor A, Geh C, Oakes S, Green C, Walker M, Newcombe N, Green S, Growcott J, Barker A, Wilkinson RW. Mol Cancer Ther. 2009 Jul;8(7):1856-66. doi: 10.1158/1535-7163.MCT-08-0836. Epub 2009 Jun 9.
Deregulation of the cell cycle has long been recognized as an essential driver of tumorigenesis, and agents that selectively target key cell cycle components continue to hold promise as potential therapeutics. We have developed AZD5438, a 4-(1-isopropyl-2-methylimidazol-5-yl)-2-(4-methylsulphonylanilino) pyrimidine, as a potent inhibitor of cyclin-dependent kinase (cdk) 1, 2, and 9 (IC(50), 16, 6, and 20 nmol/L, respectively). In vitro, AZD5438 showed significant antiproliferative activity in human tumor cell lines (IC(50) range, 0.2-1.7 micromol/L), causing inhibition of the phosphorylation of cdk substrates pRb, nucleolin, protein phosphatase 1a, and RNA polymerase II COOH-terminal domain and blocking cell cycling at G(2)-M, S, and G(1) phases. In vivo, when orally administered at either 50 mg/kg twice daily or 75 mg/kg once daily, AZD5438 inhibited human tumor xenograft growth (maximum percentage tumor growth inhibition, range, 38-153; P < 0.
ConcentrationVolumeMass1 mg5 mg10 mg
1 mM2.6921 mL13.4604 mL26.9208 mL
5 mM0.5384 mL2.6921 mL5.3842 mL
10 mM0.2692 mL1.3460 mL2.6921 mL
50 mM0.0538 mL0.2692 mL0.5384 mL

AZD5438 is a kinase ligand scaffold that may support CDK-oriented degrader design. Linker installation should be directed away from the heteroaryl kinase-recognition core.

Structure: AZD5438 is a kinase-inhibitor scaffold containing an indole/azaindole-like fused heteroaromatic core, a chloromethoxy-substituted aryl group, and a morpholinyl ethyl amide side chain. The structure includes heteroaryl nitrogens, an amide carbonyl, and a tertiary morpholine that may influence polarity and solubility.

Reactivity: For PROTAC construction, the morpholine-containing side-chain region or amide-associated periphery is more suitable for linker exploration than the fused heteroaryl kinase-binding core. Alkyl, PEG, amide, carbamate, or tertiary-amine-compatible linkers can be evaluated with CRBN, VHL, or IAP ligands. Preservation of the heteroaryl recognition elements and aryl substitution pattern is recommended until kinase-binding tolerance is experimentally confirmed.

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Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2

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Tip: Chemical formula is case sensitive. C22H30N4O c22h30n40
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