Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63061.23 
• Atom Count: 4355 
• Residue Count: 555 
• Unique protein chains: 1

1ZD4

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

• DOI: 10.2210/pdb1ZD4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2005-04-14 Released: 2006-03-07 
• Deposition Author(s): Gomez, G.A., Morisseau, C., Hammock, B.D., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.283 
• R-Value Work: 0.233 

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

• PubMed: 16322563 
• DOI: 10.1110/ps.051720206
• Primary Citation of Related Structures:  
  1ZD5, 1ZD3, 1ZD2


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
epoxide hydrolase 2, cytoplasmic	A	555	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NC6	A	6-{[(CYCLOHEXYLAMINO)CARBONYL]AMINO}HEXANOIC ACID 4-(3-CYCLOHEXYLURIEDO)-HEXANOIC ACID C13 H24 N2 O3 KFTVEPYSUSWBRD-UHFFFAOYSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NC6	IC50: >100000 nM (100) BINDINGDB
NC6	IC50: 253000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.283 
• R-Value Work: 0.233 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 92.970	α = 90.00
b = 92.970	β = 90.00
c = 246.120	γ = 120.00

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
AMoRE	phasing
CrystalClear	data reduction
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-14 
• Released Date: 2006-03-07 
• Deposition Author(s): Gomez, G.A., Morisseau, C., Hammock, B.D., Christianson, D.W.

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
• Version 1.3: 2018-04-04
  Type: Data collection