Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.26 kDa 
• Atom Count: 5355 
• Residue Count: 632 
• Unique protein chains: 1

4X6X

Human soluble epoxide hydrolase in complex with a three substituted cyclopropane derivative

• DOI: 10.2210/pdb4X6X/pdb

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


• Deposited: 2014-12-09 Released: 2015-04-08 
• Deposition Author(s): Chiyo, N., Takai, K., Ishii, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Three-dimensional rational approach to the discovery of potent substituted cyclopropyl urea soluble epoxide hydrolase inhibitors.

Takai, K., Chiyo, N., Nakajima, T., Nariai, T., Ishikawa, C., Nakatani, S., Ikeno, A., Yamamoto, S., Sone, T.

(2015) Bioorg Med Chem Lett 25: 1705-1708

• PubMed: 25800114 
• DOI: 10.1016/j.bmcl.2015.02.076
• Structures With Same Primary Citation


• PubMed Abstract: 
  

We have previously reported a series of cyclopropyl urea derivatives as potent orally available soluble epoxide hydrolase (sEH) inhibitors. Here, we designed and synthesized three substituted cyclopropane derivatives that occupy all available pockets of sEH catalytic domain. Compound 14 with a diphenyl substituted cyclopropyl moiety showed good sEH inhibitory activity. Co-crystal structure of this compound and human sEH hydrolase catalytic domain revealed enzyme pockets occupied by the phenoxypiperidine part and the diphenyl cyclopropyl moiety. Furthermore, investigation of the phenoxypiperidine part of compound 14 resulted in the discovery of compound 19, which showed potent sEH inhibitory activity (sub-nM sEH IC50 values).

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Organizational Affiliation: 

Drug Research Division, Sumitomo Dainippon Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka-city, Osaka 554-0022, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bifunctional epoxide hydrolase 2	A, B	336	Homo sapiens	Mutation(s): 0  Gene Names: EPHX2 EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (UniProt)
Find proteins for P34913 (Homo sapiens) Explore P34913  Go to UniProtKB:  P34913
NIH Common Fund Data Resources
PHAROS  P34913 GTEx  ENSG00000120915

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S74	A, B	3-{4-[(1-{[(1s,2R,3S)-2,3-diphenylcyclopropyl]carbamoyl}piperidin-4-yl)oxy]phenyl}propanoic acid C30 H32 N2 O4 VQQDJLMIDZHNMF-WLNZHLEZSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
S74	IC50:  2.299999952316284   nM  BindingDB
S74	IC50:  2.299999952316284   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.222 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.406	α = 90
b = 80.544	β = 125.7
c = 88.253	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-12-09 
• Released Date: 2015-04-08 
Deposition Author(s): Chiyo, N., Takai, K., Ishii, T.

Revision History 

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy