6HGW | pdb_00006hgw

Soluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4-phenoxybenzyl)ethanamine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.239 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted G3WClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history. 


Literature

Soluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4-phenoxybenzyl)ethanamine

Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G3W
Query on G3W
Download Ideal Coordinates CCD File 
B [auth A]2-(4-fluorophenyl)-~{N}-[(4-phenoxyphenyl)methyl]ethanamine
C21 H20 F N O
BPPBYUPUAFZCNN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G3W BindingDB:  6HGW IC50: 3600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.18α = 90
b = 92.42β = 90
c = 106.53γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted G3WClick on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
GermanyElse-Kroener-Fresenius Stiftung TRIP Graduate School

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    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