1ZD2

Human soluble epoxide hydrolase 4-(3-cyclohexyluriedo)-ethanoic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Human soluble epoxide hydrolase: structural basis of inhibition by 4-(3-cyclohexylureido)-carboxylic acids

Gomez, G.A.Morisseau, C.Hammock, B.D.Christianson, D.W.

(2006) Protein Sci. 15: 58-64

  • DOI: 10.1110/ps.051720206
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray crystal structures of human soluble epoxide hydrolase (sEH) complexed with four different dialkylurea inhibitors bearing pendant carboxylate "tails" of varying length have been determined at 2.3-3.0 A resolution. Similarities among inhibitor bi ...

    X-ray crystal structures of human soluble epoxide hydrolase (sEH) complexed with four different dialkylurea inhibitors bearing pendant carboxylate "tails" of varying length have been determined at 2.3-3.0 A resolution. Similarities among inhibitor binding modes reinforce the proposed roles of Y381 and/or Y465 as general acids that protonate the epoxide ring of the substrate in concert with nucleophilic attack of D333 at the electrophilic epoxide carbon. Additionally, the binding of these inhibitors allows us to model the binding mode of the endogenous substrate 14,15-epoxyeicosatrienoic acid. Contrasts among inhibitor binding modes include opposite orientations of inhibitor binding in the active-site hydrophobic tunnel. Alternative binding orientations observed for this series of inhibitors to human sEH, as well as the binding of certain dialkylurea inhibitors to human sEH and murine sEH, complicate the structure-based design of human sEH inhibitors with potential pharmaceutical applications in the treatment of hypertension. Thus, with regard to the optimization of inhibitor designs targeting human sEH, it is critical that human sEH and not murine sEH be utilized for inhibitor screening, and it is critical that structures of human sEH-inhibitor complexes be determined to verify inhibitor binding orientations that correlate with measured affinities.


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
epoxide hydrolase 2, cytoplasmic
P
555Homo sapiensMutation(s): 0 
Gene Names: EPHX2
Find proteins for P34913 (Homo sapiens)
Go to Gene View: EPHX2
Go to UniProtKB:  P34913
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
P
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NC3
Query on NC3

Download SDF File 
Download CCD File 
P
N-[(CYCLOHEXYLAMINO)CARBONYL]GLYCINE
4-(3-CYCLOHEXYLURIEDO)-ETHANOIC ACID
C9 H16 N2 O3
NVORCMBCUHQRDL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NC3IC50: >100000 - >500000 nM (100) BINDINGDB
NC3IC50: >500000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.233 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.240α = 90.00
b = 92.240β = 90.00
c = 243.360γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance