6FR2 | pdb_00006fr2

Soluble epoxide hydrolase in complex with LK864


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.210 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FR2

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of polar spirocyclic orally bioavailable urea inhibitors of soluble epoxide hydrolase.

Lukin, A.Kramer, J.Hartmann, M.Weizel, L.Hernandez-Olmos, V.Falahati, K.Burghardt, I.Kalinchenkova, N.Bagnyukova, D.Zhurilo, N.Rautio, J.Forsberg, M.Ihalainen, J.Auriola, S.Leppanen, J.Konstantinov, I.Pogoryelov, D.Proschak, E.Dar'in, D.Krasavin, M.

(2018) Bioorg Chem 80: 655-667

  • DOI: https://doi.org/10.1016/j.bioorg.2018.07.014
  • Primary Citation Related Structures: 
    6FR2

  • PubMed Abstract: 

    Spirocyclic 1-oxa-9-azaspiro[5.5]undecan-4-amine scaffold was explored as a basis for the design of potential inhibitors of soluble epoxide hydrolase (sEH). Synthesis and testing of the initial SAR-probing library followed by biochemical testing against sEH allowed nominating a racemic lead compound (±)-22. The latter showed remarkable (> 0.5 mM) solubility in aqueous phosphate buffer solution, unusually low (for sEH inhibitors) lipophilicity as confirmed by experimentally determined logD 7.4 of 0.99, and an excellent oral bioavailability in mice (as well as other pharmacokinetic characteristics). Individual enantiomer profiling revealed that the inhibitory potency primarily resided with the dextrorotatory eutomer (+)-22 (IC 50 4.99 ± 0.18 nM). For the latter, a crystal structure of its complex with a C-terminal domain of sEH was obtained and resolved. These data fully validate (+)-22 as a new non-racemic advanced lead compound for further development as a potential therapeutic agent for use in such areas as cardiovascular disease, inflammation and pain.


  • Organizational Affiliation
    • Lomonosov Institute of Fine Chemical Technologies, Moscow Technological University, Moscow 117571, Russian Federation.

Macromolecule Content 

  • Total Structure Weight: 40.17 kDa 
  • Atom Count: 2,735 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 346 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2346Homo sapiensMutation(s): 0 
Gene Names: EPHX2
EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P34913 (Homo sapiens)
Explore P34913 
Go to UniProtKB:  P34913
PHAROS:  P34913
GTEx:  ENSG00000120915 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34913
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E3N
(Subject of Investigation/LOI)

Query on E3N



Download:Ideal Coordinates CCD File
B [auth A]1-[(4~{S})-9-propan-2-ylsulfonyl-1-oxa-9-azaspiro[5.5]undecan-4-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea
C21 H30 F3 N3 O5 S
BZTKUYQNORQBRG-KRWDZBQOSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.210 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.091α = 90
b = 92.18β = 90
c = 106.998γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyPR1405/2-2

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Derived calculations
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description