compound 10 [PMID: 39952925]   Click here for help

GtoPdb Ligand ID: 13749

Compound class: Synthetic organic
Comment: This compound is a small molecule that inhibits function of the brachyury transcription factor (T-box transcription factor T; TBXT) [1]. Brachyury impacts tumour growth but is minimally expressed in normal tissues. These factors make it a promising therapeutic target. Compound 10 was identified using a crystallographic fragment screening methodology.
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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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Click here for structure editor
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 8
Hydrogen bond donors 1
Rotatable bonds 8
Topological polar surface area 92.59
Molecular weight 396.44
XLogP 0.15
No. Lipinski's rules broken 0

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 CCOC(=O)C1=CN=C(N=C1C2=CC=C(C=C2)NC(=O)C3CC3)N4CCOCC4
Isomeric SMILES CCOC(=O)C1=CN=C(N=C1C2=CC=C(NC(=O)C3CC3)C=C2)N4CCOCC4
InChI InChI=1S/C21H24N4O4/c1-2-29-20(27)17-13-22-21(25-9-11-28-12-10-25)24-18(17)14-5-7-16(8-6-14)23-19(26)15-3-4-15/h5-8,13,15H,2-4,9-12H2,1H3,(H,23,26)
InChI Key RCZAQQYXCSDWBP-UHFFFAOYSA-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/)
References
1. Newman JA, Gavard AE, Imprachim N, Aitkenhead H, Sheppard HE, Te Poele R, Clarke PA, Hossain MA, Temme L, Oh HJ et al.. (2025)
Structural insights into human brachyury DNA recognition and discovery of progressible binders for cancer therapy.
Nat Commun, 16 (1): 1596. [PMID:39952925]