9F1L | pdb_00009f1l

First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 35

• PDB DOI: https://doi.org/10.2210/pdb9F1L/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-19 Released: 2024-09-11 
• Deposition Author(s): Balourdas, D.I., Edmonds, A.K., Marsh, G.P., Maple, H.J., Spencer, J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Design of ISOX-DUAL-Based Degraders Targeting BRD4 and CBP/EP300: A Case of Degrader Collapse.

Edmonds, A.K., Balourdas, D.I., Marsh, G.P., Felix, R., Brasher, B., Cooper, J., Graber-Feesl, C., Kollareddy, M., Malik, K., Stewart, H., Chevassut, T.J.T., Lineham, E., Morley, S., Fedorov, O., Bennett, J., Rajasekaran, M.B., Ojeda, S., Harrison, D.A., Ott, C.J., Joerger, A.C., Maple, H.J., Spencer, J.

(2025) J Med Chem 68: 9638-9660

• PubMed: 40244695 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c00395
• Primary Citation Related Structures: 
  9F1J, 9F1K, 9F1L, 9F1M, 9F1N


• PubMed Abstract: 
  

  Degraders with dual activity against BRD4 and CBP/EP300 were designed. A structure-guided design approach was taken to assess and test potential exit vectors on the dual BRD4 and CBP/EP300 inhibitor, ISOX-DUAL. Candidate degrader panels revealed that VHL-recruiting moieties could mediate dose-responsive ubiquitination of BRD4. A panel of CRBN-recruiting thalidomide-based degraders was unable to induce ubiquitination or degradation of target proteins. High-resolution protein cocrystal structures revealed an unexpected interaction between the thalidomide moiety and Trp81 on the first bromodomain of BRD4. The inability to form a ternary complex provides a potential rationale for the lack of degrader activity with these compounds, some of which have remarkable affinities close to those of (+)-JQ1, as low as 65 nM in a biochemical assay, vs 1.5 μM for their POI ligand, ISOX-DUAL. Such a "degrader collapse" may represent an under-reported mechanism by which some putative degrader molecules are inactive with respect to target protein degradation.

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Organizational Affiliation: 
• Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K.
Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Avonmouth, Bristol BS11 9QD, U.K.
Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.
Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
Bio-Techne (R&D Systems), 614 McKinley Place NE, Minneapolis 55413, United States.
Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K.
Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PS, U.K.
Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QQ, U.K.
Centre for Medicines Discovery, Nuffield Department of Medicine, NDM Research building, Old Road Campus, Oxford OX3 7FZ, U.K.
Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K.
Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States.
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.24 kDa 
• Atom Count: 1,283 
• Modeled Residue Count: 126 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H83 (Subject of Investigation/LOI)	D [auth A]	N-[2-[2-[(3R)-2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-4-yl]oxyethyl]-2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanamide C48 H57 N9 O8 XOBMVWOYBYSFGT-LDLOPFEMSA-N
EDO	B [auth A], C [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.788	α = 90
b = 43.881	β = 102.207
c = 56.333	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Balourdas, D.I., Edmonds, A.K., Marsh, G.P., Maple, H.J., Spencer, J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	JO 1473/1-3

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references, Structure summary