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 ?
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 1.0 of the entry. See complete history.

Literature

Soluble epoxide hydrolase in complex with PROTAC JSF67

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

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B]	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 K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	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 D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	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]