3KOO

Crystal Structure of soluble epoxide Hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Optimization of piperidyl-ureas as inhibitors of soluble epoxide hydrolase.

Eldrup, A.B.Soleymanzadeh, F.Farrow, N.A.Kukulka, A.De Lombaert, S.

(2010) Bioorg Med Chem Lett 20: 571-575

  • DOI: 10.1016/j.bmcl.2009.11.091
  • Primary Citation of Related Structures:  
    3KOO

  • PubMed Abstract: 
  • Inhibition of sEH is hypothesized to lead to an increase in epoxyeicosatrienoic acids resulting in the potentiation of their anti-inflammatory and vasodilatory effects. In an effort to explore sEH inhibition as an avenue for the development of vasodilatory and cardio- or renal-protective agents, a lead identified through high-throughput screening was optimized, guided by the determination of a solid state co-structure with sEH ...

    Inhibition of sEH is hypothesized to lead to an increase in epoxyeicosatrienoic acids resulting in the potentiation of their anti-inflammatory and vasodilatory effects. In an effort to explore sEH inhibition as an avenue for the development of vasodilatory and cardio- or renal-protective agents, a lead identified through high-throughput screening was optimized, guided by the determination of a solid state co-structure with sEH. Replacement of potential toxicophores was followed by optimization of cell-based potency and ADME properties to provide a new class of functionally potent sEH inhibitors with attractive in vitro metabolic profiles and high and sustained plasma exposures after oral administration in the rat.


    Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, United States. anne.eldrup@boehringer-ingelheim.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epoxide hydrolase 2A555Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
24D
Query on 24D

Download CCD File 
A
N-(2,4-dichlorobenzyl)-4-(pyrimidin-2-yloxy)piperidine-1-carboxamide
C17 H18 Cl2 N4 O2
UZEPPAOAIDTLTK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24DIC50:  15   nM  BindingDB
24DIC50:  63   nM  BindingDB
24DIC50 :  15   nM  PDBBind
24DIC50:  18   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.765α = 90
b = 91.765β = 90
c = 242.516γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-11-13 
  • Released Date: 2010-04-28 
  • Deposition Author(s): Farrow, N.A.

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance