compound 3 [PMID: 29633584]   Click here for help

GtoPdb Ligand ID: 9960

Immunopharmacology Ligand
Compound class: Synthetic organic
Comment: This compound 3 is a lead chemical scaffold for the further development of lysine demethylase 6B (KDM6B, also known as JMJD3 and Jumonji D3) inhibitors. JMJD3 is an inducible enzyme, that along with ubiquitously transcribed X chromosome tetratricopeptide repeat protein (UTX), forms the KDM6 subfamily of histone modifying enzymes, which catalyze the demethylation of lysine 27 on histone H3 (H3K27). H3K27 demethylases are involved in maintaining the epigenetic transcriptional state in replicating and postmitotic cells. Prior to the discovery of compound 3, GSK-J1 and its derivatives were the only selective KDM6 inhibitors to be reported [5-6]. Compound 3 is suitable for investigating the role of JMJD3 in normal tissues and in tissues that are altered by pathological conditions, such as cancer and inflammation.
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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 7
Hydrogen bond donors 2
Rotatable bonds 5
Topological polar surface area 131.73
Molecular weight 355.08
XLogP 2.29
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 COc1nc(OC)ncc1c1cnc2c(c1)c(ccc2C(=O)O)C(=O)O
Isomeric SMILES COc1nc(OC)ncc1c1cnc2c(c1)c(ccc2C(=O)O)C(=O)O
InChI InChI=1S/C17H13N3O6/c1-25-14-12(7-19-17(20-14)26-2)8-5-11-9(15(21)22)3-4-10(16(23)24)13(11)18-6-8/h3-7H,1-2H3,(H,21,22)(H,23,24)
InChI Key CAGSRYBLIZYFGG-UHFFFAOYSA-N
References
1. Anderton JA, Bose S, Vockerodt M, Vrzalikova K, Wei W, Kuo M, Helin K, Christensen J, Rowe M, Murray PG et al.. (2011)
The H3K27me3 demethylase, KDM6B, is induced by Epstein-Barr virus and over-expressed in Hodgkin's Lymphoma.
Oncogene, 30 (17): 2037-43. [PMID:21242977]
2. De Santa F, Narang V, Yap ZH, Tusi BK, Burgold T, Austenaa L, Bucci G, Caganova M, Notarbartolo S, Casola S et al.. (2009)
Jmjd3 contributes to the control of gene expression in LPS-activated macrophages.
EMBO J, 28 (21): 3341-52. [PMID:19779457]
3. De Santa F, Totaro MG, Prosperini E, Notarbartolo S, Testa G, Natoli G. (2007)
The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing.
Cell, 130 (6): 1083-94. [PMID:17825402]
4. Giordano A, Del Gaudio F, Johansson C, Riccio R, Oppermann U, Di Micco S. (2018)
Virtual Fragment Screening Identification of a Quinoline-5,8-dicarboxylic Acid Derivative as a Selective JMJD3 Inhibitor.
ChemMedChem, 13 (12): 1160-1164. [PMID:29633584]
5. Hu J, Wang X, Chen L, Huang M, Tang W, Zuo J, Liu YC, Shi Z, Liu R, Shen J et al.. (2016)
Design and discovery of new pyrimidine coupled nitrogen aromatic rings as chelating groups of JMJD3 inhibitors.
Bioorg Med Chem Lett, 26 (3): 721-725. [PMID:26776360]
6. Kruidenier L, Chung CW, Cheng Z, Liddle J, Che K, Joberty G, Bantscheff M, Bountra C, Bridges A, Diallo H et al.. (2012)
A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.
Nature, 488 (7411): 404-8. [PMID:22842901]
7. Ntziachristos P, Tsirigos A, Welstead GG, Trimarchi T, Bakogianni S, Xu L, Loizou E, Holmfeldt L, Strikoudis A, King B et al.. (2014)
Contrasting roles of histone 3 lysine 27 demethylases in acute lymphoblastic leukaemia.
Nature, 514 (7523): 513-7. [PMID:25132549]