CBPD-409   Click here for help

GtoPdb Ligand ID: 13301

Synonyms: CBPD409 | compound 25 [PMID: 38530938]
Compound class: Synthetic organic
Comment: CBPD-409 is an orally bioactive PROTAC degrader that targets the CBP (CREB binding protein) and p300 (E1A binding protein p300) proteins [1]. It binds to the target proteins using a GNE-049-derived moiety, and a thalidomide ligand is used to interact with the cereblon E3 ubiquitin ligase.
CBP and p300 are bromodomain and histone acetyltransferase (HAT) domain-containing proteins that act as androgen receptor transcriptional coactivators. CBPD-409 was designed to disrupt CBP/p300-induced androgen receptor expression in prostate cancers.
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 15
Hydrogen bond donors 1
Rotatable bonds 9
Topological polar surface area 144.78
Molecular weight 862.97
XLogP 2.82
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 CC(=O)N1CCC2=C(C1)C(=NN2[C@H]3CC[C@@H](CC3)CN4CCN(CC4)C5=CC=C6C(=C5)C(=O)N(C7CCC(=O)NC7=O)C6=O)N8CCCC9=CC(=C(C=C98)C(F)F)C%10=CN(C)N=C%10
Isomeric SMILES O=C1CCC(N2C(=O)C3=CC=C(C=C3C2=O)N4CCN(C[C@@H]5CC[C@H](CC5)N6N=C(N7CCCC8=C7C=C(C(C=9C=NN(C9)C)=C8)C(F)F)C%10=C6CCN(C%10)C(C)=O)CC4)C(N1)=O
InChI InChI=1S/C46H52F2N10O5/c1-27(59)55-15-13-38-37(26-55)43(56-14-3-4-29-20-34(30-23-49-52(2)25-30)35(42(47)48)22-40(29)56)51-58(38)31-7-5-28(6-8-31)24-53-16-18-54(19-17-53)32-9-10-33-36(21-32)46(63)57(45(33)62)39-11-12-41(60)50-44(39)61/h9-10,20-23,25,28,31,39,42H,3-8,11-19,24,26H2,1-2H3,(H,50,60,61)/t28-,31-,39?
InChI Key CXJGNQXWKVPWMM-KEQSSBIPSA-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
CBP/p300 degradation with DC50 0.2-0.4 nM in prostate cancer cell lines; nanomolar antiproliferative potency in AR+ve prostate cancer cell lines, with anti-tumour efficacy in the mouse VCaP xenograft model following oral administration [1].
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
CREB binding protein Hs None Binding - - - 1
⤷ PROTAC [1]
E1A binding protein p300 Hs None Binding - - - 1
⤷ PROTAC [1]