8QN0

Soluble epoxide hydrolase in complex with RK3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Photosensitization enables Pauson-Khand-type reactions with nitrenes.

Li, F.Zhu, W.F.Empel, C.Datsenko, O.Kumar, A.Xu, Y.Ehrler, J.H.M.Atodiresei, I.Knapp, S.Mykhailiuk, P.K.Proschak, E.Koenigs, R.M.

(2024) Science 383: 498-503

  • DOI: https://doi.org/10.1126/science.adm8095
  • Primary Citation of Related Structures:  
    8QMZ, 8QN0

  • PubMed Abstract: 

    The Pauson-Khand reaction has in the past 50 years become one of the most common cycloaddition reactions in chemistry. Coupling two unsaturated bonds with carbon monoxide, the transformation remains limited to CO as a C 1 building block. Herein we report analogous cycloaddition reactions with nitrenes as an N 1 unit. The reaction of a nonconjugated diene with a nitrene precursor produces bicyclic bioisosteres of common saturated heterocycles such as piperidine, morpholine, and piperazine. Experimental and computational mechanistic studies support relaying of the diradical nature of triplet nitrene into the π-system. We showcase the reaction's utility in late-stage functionalization of drug compounds and discovery of soluble epoxide hydrolase inhibitors.


  • Organizational Affiliation

    RWTH Aachen University, Institute of Organic Chemistry, Landoltweg 1, D-52074 Aachen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2
A, B
367Homo 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
WJ5 (Subject of Investigation/LOI)
Query on WJ5

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(3~{a}~{R},6~{a}~{S})-~{N}-[(2,4-dichlorophenyl)methyl]-5-(4-methylphenyl)sulfonyl-1,3,3~{a},4,6,6~{a}-hexahydropyrrolo[3,4-c]pyrrole-2-carboxamide
C21 H23 Cl2 N3 O3 S
SCQXAOYLXUOAEA-CALCHBBNSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
H [auth B]
I [auth B]
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.332α = 90
b = 80.478β = 92.14
c = 90.038γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
MOLREPphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany515365930
German Research Foundation (DFG)Germany448583558
German Research Foundation (DFG)Germany505561502

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release