9VEQ | pdb_00009veq

Crystal structure of Keap1 in complex with a small molecule inhibitor, KMN003

• PDB DOI: https://doi.org/10.2210/pdb9VEQ/pdb

• Classification: PEPTIDE BINDING PROTEIN/INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-10 Released: 2025-11-12 
• Deposition Author(s): Ishida, H., Osawa, M.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

KMN003 activates Nrf2 via disruption of the Keap1-Nrf2 interaction and p38-dependent transcriptional regulation

Komada, K., Toyoshima, K., Yasuda, D., Ishida, H., Kojima, K., Osawa, M., Hirano, T., Ohe, T., Tago, K., Funakoshi-Tago, M.

(2025) Cell Signal 

• DOI: https://doi.org/10.1016/j.cellsig.2025.112194

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.62 kDa 
• Atom Count: 4,987 
• Modeled Residue Count: 570 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B	290	Mus musculus	Mutation(s): 0  Gene Names: Keap1, Inrf2, Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus) Explore Q9Z2X8  Go to UniProtKB:  Q9Z2X8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L98 (Subject of Investigation/LOI)	C [auth A], E [auth B]	4-[1,4-bis[(4-ethoxyphenyl)sulfonylamino]naphthalen-2-yl]butanoic acid C30 H32 N2 O8 S2 KVAYHZPJAGMVIR-UHFFFAOYSA-N
FMT	D [auth A], F [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.81	α = 90
b = 75.199	β = 105.1
c = 110.368	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Ishida, H., Osawa, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	22K07131
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24K02169

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release