ziftomenib   Click here for help

GtoPdb Ligand ID: 11680

Synonyms: compound 151 [US10781218B2] | KO-539 | KO539
PDB Ligand
Compound class: Synthetic organic
Comment: We obtained the chemical structure for ziftomenib from WHO Proposed list 125 of July 2021. This mapped to PubChem CID 138497449, and to the small molecule KO-539 (Kura Oncology). KO-539 is an orally bioavailable, clinical stage agent that was designed to disrupt the protein-protein interaction between tumour suppressor menin (MEN1, O00255) and MLL oncoproteins (re-arranged lysine (K)-specific methyltransferases) as a mechanism to treat acute myeloid leukemia (AML) [1,4]. The menin-MLL interaction is an essential upregulator of the expression of genes such as HOXA9 and MEIS1 that are involved in the development of AML. Blocking the menin-MLL interaction is predicted to induce terminal differentiation of AML blasts by reducing transcription of the HOXA9 and MEIS1 AML promoters. KO-539 binds to menin [3].

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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 10
Hydrogen bond donors 2
Rotatable bonds 11
Topological polar surface area 159.04
Molecular weight 717.29
XLogP 4.73
No. Lipinski's rules broken 1

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 CNc1nc(NC2CCN(CC2)Cc2ccc3c(c2C)cc(n3C[C@@H](N2CCN(CC2)S(=O)(=O)C)C)C#N)c2c(n1)sc(c2)CC(F)(F)F
Isomeric SMILES Cc1c(ccc2c1cc(n2C[C@H](C)N1CCN(CC1)S(=O)(=O)C)C#N)CN1CCC(CC1)Nc1c2cc(sc2nc(n1)NC)CC(F)(F)F
InChI InChI=1S/C33H42F3N9O2S2/c1-21(43-11-13-44(14-12-43)49(4,46)47)19-45-25(18-37)15-27-22(2)23(5-6-29(27)45)20-42-9-7-24(8-10-42)39-30-28-16-26(17-33(34,35)36)48-31(28)41-32(38-3)40-30/h5-6,15-16,21,24H,7-14,17,19-20H2,1-4H3,(H2,38,39,40,41)/t21-/m0/s1
InChI Key BGGALFIXXQOTPY-NRFANRHFSA-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/)
Bioactivity Comments
KO-539 displaces binding of MLL to menin with an IC50 of <50 nM, in a fluorescence polarization assay [3].