Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.00 kDa 
• Atom Count: 4377 
• Modelled Residue Count: 545 
• Deposited Residue Count: 555 
• Unique protein chains: 1

3I1Y

Crystal Structure of soluble epoxide Hydrolase

• PDB DOI: 10.2210/pdb3I1Y/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-28 Released: 2009-10-13 
• Deposition Author(s): Farrow, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.292 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Structure-based optimization of arylamides as inhibitors of soluble epoxide hydrolase.

Eldrup, A.B., Soleymanzadeh, F., Taylor, S.J., Muegge, I., Farrow, N.A., Joseph, D., McKellop, K., Man, C.C., Kukulka, A., De Lombaert, S.

(2009) J Med Chem 52: 5880-5895

• PubMed: 19746975 
• DOI: 10.1021/jm9005302
• Primary Citation of Related Structures:  
  3I1Y, 3I28


• PubMed Abstract: 
  

Inhibition of soluble epoxide hydrolase (sEH) is hypothesized to lead to an increase in circulating levels of epoxyeicosatrienoic acids, resulting in the potentiation of their in vivo pharmacological properties. As part of an effort to identify inhibitors of sEH with high and sustained plasma exposure, we recently performed a high throughput screen of our compound collection. The screen identified N-(3,3-diphenyl-propyl)-nicotinamide as a potent inhibitor of sEH. Further profiling of this lead revealed short metabolic half-lives in microsomes and rapid clearance in the rat. Consistent with these observations, the determination of the in vitro metabolic profile of N-(3,3-diphenyl-propyl)-nicotinamide in rat liver microsomes revealed extensive oxidative metabolism and a propensity for metabolite switching. Lead optimization, guided by the analysis of the solid-state costructure of N-(3,3-diphenyl-propyl)-nicotinamide bound to human sEH, led to the identification of a class of potent and selective inhibitors. An inhibitor from this class displayed an attractive in vitro metabolic profile and high and sustained plasma exposure in the rat after oral administration.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals, Ridgefield, Connecticut 06877, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase 2	A	555	Homo sapiens	Mutation(s): 0  Gene Names: EPHX2 EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens) Explore P34913  Go to UniProtKB:  P34913
PHAROS:  P34913

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
33N	B [auth A]	N-(3,3-diphenylpropyl)pyridine-3-carboxamide C21 H20 N2 O GDHXZIQAOUBZCC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
33N	PDBBind:  3I1Y	IC50: 7 (nM) from 1 assay(s)
	Binding MOAD:  3I1Y	IC50: 7 (nM) from 1 assay(s)
	BindingDB:  3I1Y	IC50: 7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 0.292 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.609	α = 90
b = 92.609	β = 90
c = 244.046	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-28 
• Released Date: 2009-10-13 
Deposition Author(s): Farrow, N.A.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-24
  Changes: Derived calculations