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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.292 (Depositor), 0.294 (DCC)
R-Value Work:
0.220 (Depositor), 0.221 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1080/14756366.2025.2574990
Primary Citation 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.

Organizational Affiliation

Laboratori de Química Farmacèutica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34913
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H8Y (Subject of Investigation/LOI) Query on A1H8Y Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.292 (Depositor), 0.294 (DCC)
R-Value Work: 0.220 (Depositor), 0.221 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.