PF-06821497   Click here for help

GtoPdb Ligand ID: 10516

Synonyms: compound 23a [PMID: 29211475] | PF06821497
PDB Ligand
Compound class: Synthetic organic
Comment: PF-06821497 is an orally active inhibitor of the histone methyltransferase, enhancer of zeste homolog 2 (EZH2), that was developed by Pfizer for antineoplastic potential [1]. Inhibition of EZH2 activity reduces mono-, di-, and trimethylation of lysine 27 on histone H3 (H3K27me, me2, and me3), and this ultimately leads to an antiproliferative effect on susceptible cancer cells (i.e. where aberrant EZH2-mediated epigenetic alterations are driving tumour initiation and progression).
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species
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 CDK toolkit. 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 4
Hydrogen bond donors 1
Rotatable bonds 6
Topological polar surface area 80.86
Molecular weight 466.11
XLogP 3.04
No. Lipinski's rules broken 0
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.

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Canonical SMILES COC(c1cc(Cl)c2c(c1Cl)C(=O)N(CC2)Cc1c(OC)cc([nH]c1=O)C)C1COC1
Isomeric SMILES CO[C@@H](c1cc(Cl)c2c(c1Cl)C(=O)N(CC2)Cc1c(OC)cc([nH]c1=O)C)C1COC1
InChI InChI=1S/C22H24Cl2N2O5/c1-11-6-17(29-2)15(21(27)25-11)8-26-5-4-13-16(23)7-14(19(24)18(13)22(26)28)20(30-3)12-9-31-10-12/h6-7,12,20H,4-5,8-10H2,1-3H3,(H,25,27)/t20-/m1/s1
InChI Key RXCVUHMIWHRLDF-HXUWFJFHSA-N
Bioactivity Comments
In vitro, PF-06821497 inhibits H3K27 trimethylation in human B cell non-Hodgkin lymphoma Karpas 422 cells with an IC50 of 4 nM, and inhibits proliferation of these cells with an IC50 of 6 nM [1]. The compound is active in vivo, in mice bearing Karpas 422 DLBCL tumour xenografts. Note that EZH2 carries the activating Y641N mutation [2] in Karpas 422 cells, which elevates the enzyme's H3K27 trimethylation function.
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
enhancer of zeste 2 polycomb repressive complex 2 subunit Hs Inhibitor Inhibition >10.0 pKi - 1
⤷ pKi >10.0 (Ki <1x10-10 M) [1]
Description: Inhibition of enzyme function in a biochemical assay using the (activating) Y641N mutant form of EZH2.