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KI-CDK9d-32   Click here for help

GtoPdb Ligand ID: 13866

Compound class: Synthetic organic
Comment: KI-CDK9d-32 is a CDK9-directed PROTAC [2]. CDK9 binding is achieved by inclusion of the inhibitor KI-ARv-03 [1] (the inhibitor that was modified to become istisociclib), and pomalidomide is used as the cereblon (CRBN) ubiquitin ligase recruiting moiety. CDK9 degradation downregulates MYC protein expression and destabilizes nucleolar homeostasis.
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 3
Rotatable bonds 11
Topological polar surface area 142.05
Molecular weight 703.83
XLogP 1.31
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 CCCC1=NC2=CC=NN2C(=C1)N[C@@H]3CC[C@H](C3)NC(=O)C4=CC=C(C=C4)CN5CCN(CC5)C6=CC=C7C(=C6)CN(C8CCC(=O)NC8=O)C7=O
Isomeric SMILES CCCC1=NC2=CC=NN2C(N[C@@H]3CC[C@H](C3)NC(=O)C4=CC=C(CN5CCN(CC5)C6=CC7=C(C=C6)C(=O)N(C7)C8CCC(=O)NC8=O)C=C4)=C1
InChI InChI=1S/C39H45N9O4/c1-2-3-28-22-35(48-34(41-28)14-15-40-48)42-29-8-9-30(21-29)43-37(50)26-6-4-25(5-7-26)23-45-16-18-46(19-17-45)31-10-11-32-27(20-31)24-47(39(32)52)33-12-13-36(49)44-38(33)51/h4-7,10-11,14-15,20,22,29-30,33,42H,2-3,8-9,12-13,16-19,21,23-24H2,1H3,(H,43,50)(H,44,49,51)/t29-,30-,33?/m1/s1
InChI Key DQQMOQXMKRXELC-XMOVUWPTSA-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. Richters A, Doyle SK, Freeman DB, Lee C, Leifer BS, Jagannathan S, Kabinger F, Koren JV, Struntz NB, Urgiles J et al.. (2021)
Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors.
Cell Chem Biol, 28 (2): 134-147.e14. [PMID:33086052]
2. Toure MA, Motoyama K, Xiang Y, Urgiles J, Kabinger F, Koglin AS, Iyer RS, Gagnon K, Kumar A, Ojeda S et al.. (2025)
Targeted degradation of CDK9 potently disrupts the MYC-regulated network.
Cell Chem Biol, 32 (4): 542-555.e10. [PMID:40154489]