6HGW | pdb_00006hgw

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

• PDB DOI: https://doi.org/10.2210/pdb6HGW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-23 Released: 2019-08-07 
• Deposition Author(s): Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

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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

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.97 kDa 
• Atom Count: 2,623 
• Modeled Residue Count: 319 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional epoxide hydrolase 2	A	346	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G3W	B [auth A]	2-(4-fluorophenyl)-~{N}-[(4-phenoxyphenyl)methyl]ethanamine C21 H20 F N O BPPBYUPUAFZCNN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 80.18	α = 90
b = 92.42	β = 90
c = 106.53	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Kramer, J.S., Pogoryelov, D., Hiesinger, K., Proschak, E.

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Funding Organization	Location	Grant Number
	Germany	Else-Kroener-Fresenius Stiftung TRIP Graduate School

Revision History  

• 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