9M24 | pdb_00009m24

Crystal Structure of kelch domain of human KEAP1 in complex with CH7450924


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.201 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9M24

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

CH7450924, a KEAP1-NRF2 interaction inhibitor, ameliorates LPS-induced multiple organ dysfunction via inflammatory pathway inhibition.

Hoshino, M.Yasui, Y.Mitsumata, S.Ito, Y.Kawauchi, H.Komatsu, R.Kimbara, A.Horiba, N.

(2025) Sci Rep 15: 36413-36413

  • DOI: https://doi.org/10.1038/s41598-025-20350-w
  • Primary Citation Related Structures: 
    9M24

  • PubMed Abstract: 

    Multiple organ dysfunction syndrome (MODS) claims a life every few seconds worldwide and is a severe condition that can affect people of all ages. Despite the availability of various treatments, the unmet medical needs remain high. Nuclear factor erythroid 2-related factor 2 (NRF2) is a key molecule involved in biological protection and is expected to be beneficial for MODS, but its role in ameliorating MODS remains unknown. We identified a novel kelch-like ECH-associated protein 1 (KEAP1)-NRF2 protein-protein interaction inhibitor, CH7450924, and evaluated its efficacy in lipopolysaccharide (LPS)-induced MODS models. To characterize our compound, we analyzed CH7450924 binding to KEAP1 by crystallography. Comprehensive binding and inhibition experiments were conducted to evaluate selectivity. Subsequently, we assessed its therapeutic effects using an LPS-induced MODS mouse model. In the MODS model, survival rate, inflammatory markers, organ function, microcirculation, and histopathology were assessed. The results demonstrated that CH7450924 bound non-covalently to KEAP1 and competitively inhibited the KEAP1-NRF2 binding with high selectivity. In the MODS model, CH7450924 significantly ameliorated the mortality rate. CH7450924 significantly decreased plasma IL-6, IL-1β, and TNFα and suppressed inflammatory cytokine mRNA expression in kidney and liver. CH7450924 improved kidney function and liver injury as indicated by plasma biochemistry. While not affecting blood pressure or heart rate, CH7450924 significantly improved peripheral blood flow in the ear. CH7450924 also significantly increased platelet count and reduced plasma PAI-1. Endothelial damage markers were also reduced in kidney and liver. In a lung injury model induced by intratracheal LPS injection, CH7450924 significantly reduced inflammation, prevented structural damage, and improved respiratory function. In conclusion, this study reveals that NRF2 activation is critical for the treatment for MODS. CH7450924, a highly potent and selective NRF2 activator, ameliorated MODS by protecting kidney, liver, and lung through its anti-inflammatory properties and its ability to protect against endothelial damage and organ dysfunction.


  • Organizational Affiliation
    • Chugai Research Institute for Medical Science, Inc., Kanagawa, Japan. hoshinomsk@chugai-pharm.co.jp.

Macromolecule Content 

  • Total Structure Weight: 33.64 kDa 
  • Atom Count: 2,696 
  • Modeled Residue Count: 285 
  • Deposited Residue Count: 293 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1293Homo sapiensMutation(s): 2 
Gene Names: KEAP1INRF2KIAA0132KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens)
Explore Q14145 
Go to UniProtKB:  Q14145
PHAROS:  Q14145
GTEx:  ENSG00000079999 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L8K
(Subject of Investigation/LOI)

Query on A1L8K



Download:Ideal Coordinates CCD File
B [auth A]4-[3-[2-chloro-4-[(2R,5R)-2,4,5-trimethylpiperazin-1-yl]benzoyl]-2,4-dihydro-1,3-benzoxazin-8-yl]-5-fluoro-2-(3-oxa-8-azabicyclo[3.2.1]octan-8-yl)benzoic acid
C35 H38 Cl F N4 O5
DDERPJUWCXEREZ-YENTXNKWSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
O [auth A],
Q [auth A],
R [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.201 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.112α = 90
b = 76.582β = 105.39
c = 48.269γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release