8S75 | pdb_00008s75

Soluble epoxide hydrolase in complex with PROTAC FL412

PDB DOI: https://doi.org/10.2210/pdb8S75/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), Fraunhofer Cluster of Excellence Immune-Mediated Diseases

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.220 (Depositor), 0.240 (DCC)
R-Value Work:
0.187 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Soluble epoxide hydrolase in complex with PROTAC FL412

Kumar, A., Schoenfeld, J., Hiesinger, K., Lillich, F., Proschak, E., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 86.47 kDa
Atom Count: 5,765
Modeled Residue Count: 640
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
A1H5L (Subject of Investigation/LOI) Query on A1H5L Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	~{N}-[2-[2-[2-[2-[2-[2-[2-[2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-4-yl]oxyethanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]-4-[4-[[4-(trifluoromethyloxy)phenyl]carbamoylamino]cyclohexyl]oxy-benzamide C₄₆ H₅₃ F₃ N₆ O₁₄ STGMSTZSBJPAMZ-YRLQYNNYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [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], J [auth A], K [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 J [auth A] Focus chain K [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 J [auth A] Focus chain K [auth B]