9F1A | pdb_00009f1a

Crystal structure of human soluble epoxide hydrolase C-terminal domain in complex with a benzohomoadamantane-based urea inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9F1A/pdb

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


• Deposited: 2024-04-18 Released: 2025-04-30 
• Deposition Author(s): Qiu, Q., Prischi, F., Jora, B., Vazquez, S., Conte, M.R.
• Funding Organization(s): King's College London

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Dimethoxybenzohomoadamantane-based soluble epoxide hydrolase inhibitors: in vivo efficacy in a murine model of chemotherapy-induced neuropathic pain.

Codony, S., Jora, B., Santos-Caballero, M., Qiu, Q., Calvo-Tusell, C., Escriche, C., Turcu, A.L., Prischi, F., Bartra, C., Val, C., Morisseau, C., Perez, B., Bertran-Mostazo, A., Osuna, S., Corpas, R., Grinan-Ferre, C., Galdeano, C., Loza, M.I., Pallas, M., Sanfeliu, C., Hammock, B.D., Brea, J., Feixas, F., Conte, M.R., Cobos, E.J., Vazquez, S.

(2025) J Enzyme Inhib Med Chem 40: 2574990-2574990

• PubMed: 41128518 
• DOI: https://doi.org/10.1080/14756366.2025.2574990
• Primary Citation of Related Structures:  
  9F1A


• PubMed Abstract: 
  

  The soluble epoxide hydrolase (sEH) has recently emerged as a promising target for the treatment of several pain-related conditions. Herein, we report the design and synthesis of a peripherally restricted sEH inhibitor with high potency and good Drug Metabolism and Pharmacokinetics (DMPK) properties. Molecular dynamics and X-ray crystallography helped reveal the binding of these inhibitors to sEH. The selected compound showed a robust analgesic effect in a dose-dependent manner in a murine model of chemotherapy-induced neuropathic pain (CINP). Moreover, the compound also prevented the development of paclitaxel-induced neuropathic pain. Overall, these results suggest that peripheral inhibition of sEH might constitute a novel therapy to prevent and treat CINP.

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Organizational Affiliation: 
• Laboratori de Química Farmacèutica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.
Institute of Biomedicine of the University of Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain.
Department of Pharmacology, Faculty of Medicine and Biomedical Research Center (Neurosciences Institute), University of Granada, Biosanitary Research Institute-ibs.GRANADA, Granada, Spain.
Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK.
Departament de Química and Institut de Química Computacional i Catàlisi (IQCC), Universitat de Girona, Girona, Spain.
Institute of Biomedical Research of Barcelona (IIBB), CSIC, Barcelona, Spain.
Innopharma Drug Screening Platform/Biofarma Research Group, CIMUS Research Center, Pharmacology Department, School of Pharmacy, University of Santiago de Compostela (USC), Santiago de Compostela, Spain.
Department of Entomology and Nematology and Comprehensive Cancer Center, University of California, Davis, CA, USA.
Department of Pharmacology, Therapeutics and Toxicology, Institute of Neurosciences, Autonomous University of Barcelona, Barcelona, Spain.
Departament de Farmàcia i Tecnología Farmacèutica, i Fisicoquímica, Universitat de Barcelona, Barcelona, Spain.
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain.
Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 80.14 kDa 
• Atom Count: 5,282 
• Modeled Residue Count: 632 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional epoxide hydrolase 2	A, B	344	Homo sapiens	Mutation(s): 0  Gene Names: EPHX2 EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens) Explore P34913  Go to UniProtKB:  P34913
PHAROS:  P34913 GTEx:  ENSG00000120915

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H8Y (Subject of Investigation/LOI)	C [auth A], D [auth B]	1-(2,3-dimethoxy-9-methyl-5,6,8,9,10,11-hexahydro-7H-5,9:7,11-dimethanobenzo[9]annulen-7-yl)-3-(1-(tetrahydro-2H-pyran-4-carbonyl)piperidin-4-yl)urea C30 H43 N3 O5 VLPVTKWHYLFBTG-AMIQKGEKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.019	α = 90
b = 81.756	β = 90.54
c = 108.112	γ = 90

Software Package:

Software Name	Purpose
xia2	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Qiu, Q., Prischi, F., Jora, B., Vazquez, S., Conte, M.R.

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Funding Organization	Location	Grant Number
King's College London	United Kingdom	--

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release
  
• Version 1.1: 2025-10-29
  Changes: Database references
• Version 1.2: 2025-11-05
  Changes: Database references