dBRD9-A   Click here for help

GtoPdb Ligand ID: 10546

Compound class: Synthetic organic
Comment: This is an analogue of dBRD9, that was designed to achieve enhanced BRD9 degradation properties [1]. Like dBRD9 it is a PROTAC (proteolysis targeting chimera). dBRD9-A is a hybrid molecule that simultaneously engages the BRD9 bromodomain and recruits E3 ligase CRL4CRBN (using a pomalidomide-based module) to target BRD9 for destruction via E3 ligase-mediated ubiquitination and proteasomal degradation.
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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 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 11
Hydrogen bond donors 3
Rotatable bonds 19
Topological polar surface area 181.27
Molecular weight 779.36
XLogP 4.49
No. Lipinski's rules broken 2

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 COc1cc(cc(c1CN(CC(=O)NCCCCCCCCNc1cccc2c1C(=O)N(C2=O)C1CCC(=O)NC1=O)C)OC)c1cn(C)c(=O)c2c1ccnc2
Isomeric SMILES COc1cc(cc(c1CN(CC(=O)NCCCCCCCCNc1cccc2c1C(=O)N(C2=O)C1CCC(=O)NC1=O)C)OC)c1cn(C)c(=O)c2c1ccnc2
InChI InChI=1S/C42H49N7O8/c1-47(23-31-34(56-3)20-26(21-35(31)57-4)30-24-48(2)40(53)29-22-43-19-16-27(29)30)25-37(51)45-18-10-8-6-5-7-9-17-44-32-13-11-12-28-38(32)42(55)49(41(28)54)33-14-15-36(50)46-39(33)52/h11-13,16,19-22,24,33,44H,5-10,14-15,17-18,23,25H2,1-4H3,(H,45,51)(H,46,50,52)
InChI Key ZDINQSNMYRVAGP-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
BRD9 is critical for cell growth of synovial sarcoma cells that are driven by the SS18-SSX fusion protein that is found in BAF (SWI/SNF) transcription complexes in these tumours. dBRD9-A-mediated BRD9 degradation has exhibited efficacy against these intractable tumour cells in vitro [1]. dBRD9-A promotes almost complete BRD9 degradation at low nanomolar concentrations (>90% degradation by 6 hours at 100 nM compound concentration in HSSY1 and SYO1 cells).
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 Hs None Binding 7.1 pIC50 - 1
⤷ pIC50 7.1 (IC50 8.31x10-8 M) [1]
Description: In vitro binding affinity determined by an AlphaScreen displacement ligand binding assay.