9DU7 | pdb_00009du7

KEAP1 BTB domain in complex with the covalent activator VVD-065

• PDB DOI: https://doi.org/10.2210/pdb9DU7/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-02 Released: 2024-10-23 
• Deposition Author(s): Bernard, S.M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.231 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.199 (DCC) 

Starting Model: experimental

Literature

A Covalent Allosteric Molecular Glue Suppresses NRF2-Dependent Cancer Growth.

Roy, N., Wyseure, T., Lo, I.C., Lu, J., Eissler, C.L., Bernard, S.M., Bok, I., Snead, A.N., Parker, A., Lo, U.G., Green, J.C., Inloes, J., Jacinto, S.R., Kuenzi, B., Pariollaud, M., Negri, K., Le, K., Horning, B.D., Ibrahim, N., Grabow, S., Panda, H., Bhatt, D.P., Wilkerson, E.M., Saeidi, S., Zolkind, P., Rush, Z., Williams, H.N., Walton, E., Pastuszka, M.K., Sigler, J.J., Tran, E., Hee, K., McLaughlin, J., Ambrus-Aikelin, G., Pollock, J., Abraham, R.T., Kinsella, T.M., Simon, G.M., Major, M.B., Weinstein, D.S., Patricelli, M.P.

(2026) Cancer Discov 16: 953-975

• PubMed: 41417010 
• DOI: https://doi.org/10.1158/2159-8290.CD-25-1187
• Primary Citation Related Structures: 
  9DU7


• PubMed Abstract: 
  

  The NRF2 transcription factor is constitutively active in cancer where it functions to maintain oxidative homeostasis and reprogram cellular metabolism. NRF2-active tumors exhibit NRF2-dependency and resistance to chemo/radiotherapy. Here we characterize VVD-065, a first-in-class NRF2 inhibitor that acts via an unprecedented allosteric molecular glue mechanism. In the absence of stress or mutation, NRF2 is rapidly degraded by the KEAP1-CUL3 ubiquitin-ligase complex. VVD-065 specifically and covalently engages Cys151 on KEAP1, which in turn promotes KEAP1-CUL3 complex formation, leading to enhancement of NRF2 degradation. Previously reported Cys151-directed compounds decrease KEAP1-CUL3 interactions and stabilize NRF2, thus establishing KEAP1_Cys151 as a tunable regulator of the KEAP1-CUL3 complex and NRF2 stability. VVD-065 inhibited NRF2-dependent tumor growth and sensitized cancers to chemo/radiotherapy, supporting an open Phase I clinical trial (NCT05954312).

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Organizational Affiliation: 
• Vividion Therapeutics (United States) San Diego United States.
Degron Therapeutics SanDiego United States.
Washington University Medical Center St. Louis, Missouri United States.
Washington University in St. Louis United States.
Washington University in St. Louis Saint Louis, MO United States.
Vividion Therapeutics United States.
Vividion Therapeutics (United States) San Diego, California United States.
sciex United States.
Genesis Therapeutics United States.
Engine Biosciences San Diego, CA United States.
Independent researcher United States.
Washington University in St. Louis St. Louis, MO United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.28 kDa 
• Atom Count: 2,138 
• Modeled Residue Count: 254 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B	137	Homo sapiens	Mutation(s): 0  Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
PHAROS:  Q14145 GTEx:  ENSG00000079999

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BCT (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-{(3S)-3-[3-(4-amino-1,3,5-triazin-2-yl)-5-chlorophenyl]morpholin-4-yl}propan-1-one C16 H18 Cl N5 O2 HFRULTGTUQPJLO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.231 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.199 (DCC) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.737	α = 90
b = 72.737	β = 90
c = 64.209	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: 2024-10-23 
Deposition Author(s): Bernard, S.M.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Database references
• Version 1.2: 2026-05-13
  Changes: Database references