9KVW | pdb_00009kvw

Crystal Structures of Keap1-compound complexes

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

  • Deposited: 2024-12-05 Released: 2025-12-10 
  • Deposition Author(s): Zhuang, C.L., Yu, R.L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 
    0.233 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Design of spiro-heterocyclic substituted diaminonaphthalene Keap1-Nrf2 protein-protein interaction inhibitors as novel anti-depressant agents.

Chen, Y.Qin, Q.Ding, W.Yu, R.Wang, R.Ji, H.Yan, J.Ma, H.Jiang, C.S.Sun, Y.Zhuang, C.

(2025) Eur J Med Chem 296: 117848-117848

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117848
  • Primary Citation Related Structures: 
    9KVW

  • PubMed Abstract: 

    Oxidative stress, inflammation and the Keap1-Nrf2 pathway are validated to be related to depression. Theoretically, modulating Keap1 and Nrf2 protein-protein interaction (PPI) should be an effective method to activate Nrf2 for the treatment of major depressive disorders. We previously reported NXPZ-2, a 1,4-diaminonaphthalene, as a Keap1-Nrf2 PPI inhibitor that exhibited promising effects in an Alzheimer's disease (AD) mouse model. However, its pharmacokinetic properties were limited. Herein, we, for the first time, developed a series of heterocyclic substituted diaminonaphthalenes by an "Escape from Flatland" strategy to improve sp 3 hybridized carbons. These compounds exhibited strong binding affinity for Keap1. A crystallographic analysis revealed the high-resolution (1.44 Å) binding of CD-10 with the Keap1 protein, elucidating the complexity of CD-10's binding mechanism. In an LPS-stimulated BV2 cell model, CD-10 demonstrated the best anti-oxidative stress and anti-inflammatory potential. Furthermore, CD-10's ability to penetrate the blood-brain barrier has been significantly improved. In a chronic unpredictable mild stress (CUMS) mouse model, treatment with CD-10 effectively alleviated anxiety and depressive behaviors and restored serum neurotransmitter levels by promoting Nrf2 nuclear translocation. Overall, our findings validate that the Keap1-Nrf2 PPI inhibitor holds promise as a preclinical candidate for the treatment of depression.


  • Organizational Affiliation
    • School of Biological Science and Technology, University of Jinan, Jinan 250022, China; The Center for Basic Research and Innovation of Medicine and Pharmacy (MOE), School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.

Macromolecule Content 

  • Total Structure Weight: 32.38 kDa 
  • Atom Count: 2,488 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1288Homo sapiensMutation(s): 0 
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EHH
(Subject of Investigation/LOI)

Query on A1EHH



Download:Ideal Coordinates CCD File
B [auth A]~{N}-[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]-3-(2-oxa-8-azaspiro[4.5]decan-8-yl)propanamide
C38 H44 N6 O9 S2
ODOXLPYUODJKBR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free:  0.233 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.584α = 90
b = 72.958β = 100.6
c = 48.057γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82022065
Ministry of Science and Technology (MoST, China)China2021YFA1302200

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Database references