I-BRD9   Click here for help

GtoPdb Ligand ID: 8397

Synonyms: compound 45 [PMID 25856009] | GSK602
PDB Ligand
Compound class: Synthetic organic
Comment: This structure was drawn from the Structural Genomics Consortium's chemical probe page for I-BRD9 [1]. I-BRD9 is the first selective tool compound which will be useful in resolving the biological function of bromodomain containing 9 (BRD9) [2]. This is a compound from the Structural Genomics Consortium's (SGC) Epigenetics Probes Collection.
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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

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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 5
Hydrogen bond donors 2
Rotatable bonds 6
Topological polar surface area 128.64
Molecular weight 497.11
XLogP 5.51
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 CCn1cc(c2cccc(c2)C(F)(F)F)c2c(c1=O)cc(s2)C(=N)NC1CCS(=O)(=O)CC1
Isomeric SMILES CCn1cc(c2cccc(c2)C(F)(F)F)c2c(c1=O)cc(s2)C(=N)NC1CCS(=O)(=O)CC1
InChI InChI=1S/C22H22F3N3O3S2/c1-2-28-12-17(13-4-3-5-14(10-13)22(23,24)25)19-16(21(28)29)11-18(32-19)20(26)27-15-6-8-33(30,31)9-7-15/h3-5,10-12,15H,2,6-9H2,1H3,(H2,26,27)
InChI Key WRUWGLUCNBMGPS-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/)
Bioactivity Comments
I-BRD9 is selective for BRD9 compared to tested homologous and related proteins [2].
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
bromodomain containing 9 Primary target of this compound Hs Inhibitor Binding 7.1 pIC50 - 2
⤷ pIC50 7.1 (IC50 7.94x10-8 M) [2]
Description: Binding affinity for endogenous BRD9 from HuT-78 cell lysates, measured in a chemoproteomic competition binding assay followed by Western blot analysis.