6WWB image
Deposition Date 2020-05-08
Release Date 2021-11-17
Last Version Date 2023-10-18
Entry Detail
PDB ID:
6WWB
Keywords:
Title:
Crystal Structure of the second bromodomain of human BRD2 in complex with the compound 3b
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.31 Å
R-Value Free:
0.14
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Bromodomain-containing protein 2
Gene (Uniprot):BRD2
Chain IDs:A
Chain Length:115
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Phenyl-Glutarimides: Alternative Cereblon Binders for the Design of PROTACs.
Angew.Chem.Int.Ed.Engl. 60 26663 26670 (2021)
PMID: 34614283 DOI: 10.1002/anie.202108848

Abstact

Targeting cereblon (CRBN) is currently one of the most frequently reported proteolysis-targeting chimera (PROTAC) approaches, owing to favorable drug-like properties of CRBN ligands, immunomodulatory imide drugs (IMiDs). However, IMiDs are known to be inherently unstable, readily undergoing hydrolysis in body fluids. Here we show that IMiDs and IMiD-based PROTACs rapidly hydrolyze in commonly utilized cell media, which significantly affects their cell efficacy. We designed novel CRBN binders, phenyl glutarimide (PG) analogues, and showed that they retained affinity for CRBN with high ligand efficiency (LE >0.48) and displayed improved chemical stability. Our efforts led to the discovery of PG PROTAC 4 c (SJ995973), a uniquely potent degrader of bromodomain and extra-terminal (BET) proteins that inhibited the viability of human acute myeloid leukemia MV4-11 cells at low picomolar concentrations (IC50 =3 pM; BRD4 DC50 =0.87 nM). These findings strongly support the utility of PG derivatives in the design of CRBN-directed PROTACs.

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