3KOO

Crystal Structure of soluble epoxide Hydrolase

• PDB DOI: https://doi.org/10.2210/pdb3KOO/pdb

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


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

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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 

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

• PubMed: 19969453 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.07 kDa 
• Atom Count: 4,369 
• Modelled Residue Count: 545 
• Deposited Residue Count: 555 
• Unique protein chains: 1

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 GTEx:  ENSG00000120915

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
24D	B [auth A]	N-(2,4-dichlorobenzyl)-4-(pyrimidin-2-yloxy)piperidine-1-carboxamide C17 H18 Cl2 N4 O2 UZEPPAOAIDTLTK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
24D	BindingDB:  3KOO	IC50: min: 15, max: 63 (nM) from 3 assay(s)
	PDBBind:  3KOO	IC50: 15 (nM) from 1 assay(s)

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 = 91.765	α = 90
b = 91.765	β = 90
c = 242.516	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2021-02-24
  Changes: Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references