8S76 | pdb_00008s76

Soluble epoxide hydrolase in complex with PROTAC JSF67

PDB DOI: https://doi.org/10.2210/pdb8S76/pdb

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

Deposited: 2024-02-29 Released: 2025-03-12
Deposition Author(s): Kumar, A., Schoenfeld, J., Hiesinger, K., Lillich, F., Proschak, E., Knapp, S., Structural Genomics Consortium (SGC)
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-Based Design of PROTACS for the Degradation of Soluble Epoxide Hydrolase.

Schonfeld, J., Brunst, S., Ciomirtan, L., Willmer, L., Chromik, M.A., Kumar, A., Froemel, T., Liebisch, N., Hackspacher, A., Ehrler, J.H.M., Wintermeier, L., Hesse, C., Fiedler, J., Heering, J., Freitag, H., Zardo, P., Fieguth, H.G., Bruggerhoff, A., Jakob, J., Haupl, B., Weizel, L., Kaiser, A., Schubert-Zsilavecz, M., Oellerich, T., Fleming, I., Schebb, N.H., Furst, R., Kannt, A., Knapp, S., Proschak, E., Hiesinger, K.

(2025) J Med Chem 68: 13728-13749

PubMed: 40532036 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.5c00552
Primary Citation Related Structures:
8S76, 8S77

PubMed Abstract:
The bifunctional soluble epoxide hydrolase (sEH) represents a promising target for inflammation-related diseases. Although potent inhibitors targeting each domain are available, sEH-PROTACs offer the unique ability to simultaneously block both enzymatic functions, mimicking the sEH knockout phenotype, which has been associated with reducing inflammation, including neuroinflammation, and delaying the progression of Alzheimer's disease. Herein, we report the structure-based development of a potent sEH-PROTAC as a useful pharmacological tool. In order to facilitate a rapid testing of the PROTACs, a cell-based sEH degradation assay was developed utilizing HiBiT technology. We designed and synthesized 24 PROTACs. Furthermore, cocrystallization of sEH with two selected PROTACs allowed us to explore the binding mode and rationalize the most optimal linker length. After comprehensive biological and physicochemical characterization of this series, the most optimal PROTAC 23 was identified in primary human and murine cells, highlighting the potential of using 23 in disease-relevant cell and tissue models.

Organizational Affiliation

Institute of Pharmaceutical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 86.98 kDa
Atom Count: 5,852
Modeled Residue Count: 642
Deposited Residue Count: 734
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional epoxide hydrolase 2	A, B	367	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H5M (Subject of Investigation/LOI) Query on A1H5M Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], M [auth B]	~{N}-[[4-[3-[1-[2-[2-[2-[[2-[2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-5-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethyl]-1,2,3-triazol-4-yl]propylsulfonylamino]-2-(trifluoromethyl)phenyl]methyl]-1-[(3-fluorophenyl)methyl]indole-5-carboxamide C₄₈ H₄₅ F₄ N₉ O₁₀ S LLKXZXOMWQVKAU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], Q [auth B], R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]