KI-CDK9d-32

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

Home
Ligands
KI-CDK9d-32

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

Physico-chemical Properties

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

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/)