6HGX

Soluble epoxide hydrolase in complex with 1-(4-((4-(tert-butyl)morpholin-2-yl)methoxy)phenyl)-3-cyclohexylurea

• PDB DOI: https://doi.org/10.2210/pdb6HGX/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-23 Released: 2019-07-03 
• Deposition Author(s): Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.254 
• R-Value Work: 0.202 
• R-Value Observed: 0.207 

Literature

Computer-Aided Selective Optimization of Side Activities of Talinolol.

Hiesinger, K., Kramer, J.S., Achenbach, J., Moser, D., Weber, J., Wittmann, S.K., Morisseau, C., Angioni, C., Geisslinger, G., Kahnt, A.S., Kaiser, A., Proschak, A., Steinhilber, D., Pogoryelov, D., Wagner, K., Hammock, B.D., Proschak, E.

(2019) ACS Med Chem Lett 10: 899-903

• PubMed: 31223445 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00075
• Primary Citation of Related Structures:  
  6HGV, 6HGX


• PubMed Abstract: 
  

  Selective optimization of side activities is a valuable source of novel lead structures in drug discovery. In this study, a computer-aided approach was used to deorphanize the pleiotropic cholesterol-lowering effects of the beta-blocker talinolol, which result from the inhibition of the enzyme soluble epoxide hydrolase (sEH). X-ray structure analysis of the sEH in complex with talinolol enables a straightforward optimization of inhibitory potency. The resulting lead structure exhibited in vivo activity in a rat model of diabetic neuropatic pain.

---

Organizational Affiliation: 

Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Strasse 9, D-60438 Frankfurt am Main, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40.06 kDa 
• Atom Count: 2,715 
• Modelled Residue Count: 319 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional epoxide hydrolase 2	A	346	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3T	C [auth A]	1-[4-[[(2~{S})-4-~{tert}-butylmorpholin-2-yl]methoxy]phenyl]-3-cyclohexyl-urea C22 H35 N3 O3 PSVUAGRHPQWOOO-FQEVSTJZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
G3T	Binding MOAD:  6HGX	IC50: 77 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.254 
• R-Value Work: 0.202 
• R-Value Observed: 0.207 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.8	α = 90
b = 92	β = 90
c = 105.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

---

Funding Organization	Location	Grant Number
	Germany	Else-Kroener-Fresenius Stiftung TRIP Graduate School

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2021-02-24
  Changes: Derived calculations
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description