KDM5 inhibitor N71   Click here for help

GtoPdb Ligand ID: 10141

Compound class: Synthetic organic
Comment: N71 is a potent, selective and irreversible inhibitor of the protein lysine demethylases KDM5A and KDM5B [2]. It was designed to interact and form a covalent bond with Cys481 of KDM5 enzymes which is a cysteine residue that is located near the enzymes' active site that is present in all 4 KDM5 family enzymes but not in other dioxygenases such as the KDM4 and KDM6 histone demethylases [1]. KDM5A and KDM5B are known oncogenic drivers whose inhibition is of interest to those developing novel anti-cancer therapeutics.
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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 8
Hydrogen bond donors 2
Rotatable bonds 12
Topological polar surface area 123.24
Molecular weight 522.23
XLogP 2.26
No. Lipinski's rules broken 1
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 CN(CC=CC(=O)Nc1cccc(c1)C(c1cc2c(s1)c(ccn2)C(=O)O)OCCN1CCCCC1)C
Isomeric SMILES CN(C/C=C/C(=O)Nc1cccc(c1)C(c1cc2c(s1)c(ccn2)C(=O)O)OCCN1CCCCC1)C
InChI InChI=1S/C28H34N4O4S/c1-31(2)13-7-10-25(33)30-21-9-6-8-20(18-21)26(36-17-16-32-14-4-3-5-15-32)24-19-23-27(37-24)22(28(34)35)11-12-29-23/h6-12,18-19,26H,3-5,13-17H2,1-2H3,(H,30,33)(H,34,35)/b10-7+
InChI Key KIIDGZQVWULCMZ-JXMROGBWSA-N
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
lysine demethylase 5B Primary target of this compound Hs Inhibitor Irreversible inhibition 6.7 pIC50 - 2
⤷ pIC50 6.7 (IC50 2.2x10-7 M) [2]
Description: AlphaLISA derived IC50 values of the inhibition of KDM5B-mediated histone demethylation.
lysine demethylase 5A Primary target of this compound Hs Inhibitor Irreversible inhibition 6.5 pIC50 - 2
⤷ pIC50 6.5 (IC50 3.2x10-7 M) [2]
Description: AlphaLISA derived IC50 values of the inhibition of KDM5A-mediated histone demethylation.
lysine demethylase 4A Hs Inhibitor Inhibition 5.3 pIC50 - 2
⤷ pIC50 5.3 (IC50 5.3x10-6 M) [2]
lysine demethylase 6A Hs Inhibitor Inhibition <4.2 pIC50 - 2
⤷ pIC50 <4.2 (IC50 >6x10-5 M) [2]