4X6Y

Human soluble epoxide hydrolase in complex with a cyclopropyl urea derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2015.02.076
  • Primary Citation of Related Structures:  

  • 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 ...

    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).


    Organizational Affiliation

    Drug Research Division, Sumitomo Dainippon Pharma Co., Ltd, 3-1-98 Kasugade-naka, Konohana-ku, Osaka-city, Osaka 554-0022, Japan. Electronic address: kentaro-takai@ds-pharma.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional epoxide hydrolase 2
A, B
336Homo sapiensMutation(s): 0 
Gene Names: EPHX2
Find proteins for P34913 (Homo sapiens)
Go to Gene View: EPHX2
Go to UniProtKB:  P34913
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S94
Query on S94

Download SDF File 
Download CCD File 
A, B
4-phenoxy-N-[(1S,2R)-2-phenylcyclopropyl]piperidine-1-carboxamide
C21 H24 N2 O2
SAKQSHLUPVUJDT-UXHICEINSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S94IC50: 18 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 129.228α = 90.00
b = 80.722β = 126.22
c = 87.326γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references