8QMZ | pdb_00008qmz

Soluble epoxide hydrolase in complex with RK4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.214 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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 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.

Macromolecule Content 

  • Total Structure Weight: 170.67 kDa 
  • Atom Count: 11,567 
  • Modeled Residue Count: 1,278 
  • Deposited Residue Count: 1,468 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2
A, B, C, D
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
W6O
(Subject of Investigation/LOI)

Query on W6O



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
P [auth C],
S [auth D]
(3~{a}~{R},6~{a}~{S})-~{N}-[(2,4-dichlorophenyl)methyl]-2-(4-methylphenyl)sulfonyl-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-5-carboxamide
C22 H24 Cl2 N2 O3 S
LGIZBXBXVOKOLX-BCDXTJNWSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.214 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.29α = 90
b = 90.642β = 90
c = 188.416γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

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