9ZYT | pdb_00009zyt

Crystal Structure of BRD4 Bromodomain BD1 in Complex with Small Molecule PLX-3618

• PDB DOI: https://doi.org/10.2210/pdb9ZYT/pdb

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


• Deposited: 2026-01-06 Released: 2026-04-22 
• Deposition Author(s): Leriche, G., Barmare, F., Toth, J.I., Jamborcic, A., Kampert, T.L., Steadman, K., Yang, L., Fish, S., Daniele, E., McCarrick, M., Kallel, E.A., Li, X., Thompson, P.A., Parker, G.S., Freeman-Cook, K., Bailey, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.165 (DCC) 

Starting Model: experimental

Literature

Discovery and Structural Optimization of BRD4-Selective Monovalent Direct Degraders.

Leriche, G., Barmare, F., Toth, J.I., Jamborcic, A., Kampert, T.L., Steadman, K., Yang, L., Fish, S., Daniele, E., McCarrick, M., Kallel, E.A., Li, X., Thompson, P.A., Parker, G.S., Freeman-Cook, K., Bailey, S.

(2026) ACS Med Chem Lett 17: 1106-1113

• PubMed: 42157816 
• DOI: https://doi.org/10.1021/acsmedchemlett.6c00022
• Primary Citation Related Structures: 
  9ZYT


• PubMed Abstract: 
  

  Targeted protein degradation (TPD) via the ubiquitin-proteasome system (UPS) is a rapidly advancing drug discovery strategy that enables the selective elimination of pathogenic proteins using small molecules. Here, we report the discovery of BRD4-selective monovalent direct degraders acting through DCAF11, identified by ultrahigh-throughput screening and subsequently optimized through a structure-guided medicinal chemistry campaign. Structure-activity relationship (SAR) studies support a direct degrader mechanism and culminated in the identification of the orally bioavailable compound PLX-4104 . In vitro, PLX-4104 induces rapid, complete, and selective degradation of BRD4 and exhibits potent antiproliferative activity in acute myeloid leukemia (AML) models. In vivo, PLX-4104 treatment resulted in complete tumor regression in the AML MV-4-11 xenograft model. Collectively, this lays the groundwork for the rational development of monovalent direct degraders with applications extending beyond BRD4.

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Organizational Affiliation: 
• Plexium, 9330 Scranton Road, San Diego, California 92121, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.41 kDa 
• Atom Count: 2,518 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A [auth AAA], B [auth BBB]	124	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
A1C4W (Subject of Investigation/LOI)	D [auth AAA], F [auth BBB], G [auth BBB]	PLX-3618 C32 H27 N9 O2 S KGEBVZGNEUJHIO-VWLOTQADSA-N
EDO	C [auth AAA], E [auth BBB]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.165 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.198	α = 90
b = 115.853	β = 90.119
c = 39.045	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Leriche, G., Barmare, F., Toth, J.I., Jamborcic, A., Kampert, T.L., Steadman, K., Yang, L., Fish, S., Daniele, E., McCarrick, M., Kallel, E.A., Li, X., Thompson, P.A., Parker, G.S., Freeman-Cook, K., Bailey, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-06-03
  Changes: Database references