8QZD | pdb_00008qzd

Soluble epoxide hydrolase in complex with Epoxykinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator.

Dotsch, L.Davies, C.Hennes, E.Schonfeld, J.Kumar, A.Guita, C.D.C.L.Ehrler, J.H.M.Hiesinger, K.Thavam, S.Janning, P.Sievers, S.Knapp, S.Proschak, E.Ziegler, S.Waldmann, H.

(2024) J Med Chem 67: 4691-4706

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02245
  • Primary Citation Related Structures: 
    8QZD

  • PubMed Abstract: 

    Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes of action (MMOA). Herein, we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-γ (IFN-γ) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.


  • Organizational Affiliation
    • Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany.

Macromolecule Content 

  • Total Structure Weight: 43.22 kDa 
  • Atom Count: 3,013 
  • Modeled Residue Count: 320 
  • Deposited Residue Count: 367 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2367Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34913
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XDZ
(Subject of Investigation/LOI)

Query on XDZ



Download:Ideal Coordinates CCD File
J [auth A]2-[5-bromanyl-3-[2,2,2-tris(fluoranyl)ethanoyl]indol-1-yl]-N-cycloheptyl-ethanamide
C19 H20 Br F3 N2 O2
LJWGWJLCHFYATI-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
M [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth A],
L [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
XDZ BindingDB:  8QZD IC50: min: 6.7, max: 159 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.924α = 90
b = 80.312β = 90
c = 89.084γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionEFRE-0200481
Innovative Medicines InitiativeSwitzerland115489
European Communitys Seventh Framework ProgrammeEuropean UnionFP7/2007-2013

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Database references