dBRD9   Click here for help

GtoPdb Ligand ID: 10545

Synonyms: Naphthiridinone degrader 6 [1]
Compound class: Synthetic organic
Comment: dBRD9 is a targeted BRD9 degrader molecule [1]. It is a bifunctional molecule that simultaneously engages the BRD9 bromodomain and cereblon (CRBN; a component of the E3 ubiquitin ligase complex) to trigger BRD9 ubiquitination and proteasomal degradation. Such molecules can be described as PROTACs (proteolysis targeting chimeras). Cereblon engagement is mediated by the probe's pomalidomide module, and BRD9 recruitment is achieved by an optimised BRD9 ligand. dBRD9 is suitable as a tool/probe to interrogate BRD9's biological role and therapeutic potential.
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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

dBRD9 is commercially available from our sponsors

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 13
Hydrogen bond donors 3
Rotatable bonds 19
Topological polar surface area 199.73
Molecular weight 783.32
XLogP 1.54
No. Lipinski's rules broken 2
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 COc1cc(cc(c1CN(CC(=O)NCCOCCOCCNc1cccc2c1C(=O)N(C2=O)C1CCC(=O)NC1=O)C)OC)c1cn(C)c(=O)c2c1ccnc2
Isomeric SMILES COc1cc(cc(c1CN(CC(=O)NCCOCCOCCNc1cccc2c1C(=O)N(C2=O)C1CCC(=O)NC1=O)C)OC)c1cn(C)c(=O)c2c1ccnc2
InChI InChI=1S/C40H45N7O10/c1-45(21-29-32(54-3)18-24(19-33(29)55-4)28-22-46(2)38(51)27-20-41-11-10-25(27)28)23-35(49)43-13-15-57-17-16-56-14-12-42-30-7-5-6-26-36(30)40(53)47(39(26)52)31-8-9-34(48)44-37(31)50/h5-7,10-11,18-20,22,31,42H,8-9,12-17,21,23H2,1-4H3,(H,43,49)(H,44,48,50)
InChI Key AIOCFZJGGGEWDK-UHFFFAOYSA-N
Bioactivity Comments
dBRD9 deos not induce degradation of the BET bromodomain-containing proteins BRD4 or BRD7 [1]. It retains activity against the IKZF family of linage specific transcription factors that are validated targets of the immune-modulatory drug pomalidomide.
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
cereblon Hs None Binding 7.5 pIC50 - 1
⤷ pIC50 7.5 (IC50 3.13x10-8 M) [1]
Description: AlphaScreen competitive ligand binding assay using the CRBN-DDB1 complex.
bromodomain containing 9 Hs None Binding 7.0 pIC50 - 1
⤷ pIC50 7.0 (IC50 1.04x10-7 M) [1]
Description: AlphaScreen competitive ligand binding assay using recombinant BRD9.