4J03

Crystal structure of human soluble epoxide hydrolase complexed with fulvestrant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibition of soluble epoxide hydrolase by fulvestrant and sulfoxides.

Morisseau, C.Pakhomova, S.Hwang, S.H.Newcomer, M.E.Hammock, B.D.

(2013) Bioorg Med Chem Lett 23: 3818-3821

  • DOI: 10.1016/j.bmcl.2013.04.083
  • Primary Citation of Related Structures:  
    4J03

  • PubMed Abstract: 
  • The soluble epoxide hydrolase (sEH) is a key enzyme in the metabolism of epoxy-fatty acids, signaling molecules involved in numerous biologies. Toward finding novel inhibitors of sEH, a library of known drugs was tested for inhibition of sEH. We foun ...

    The soluble epoxide hydrolase (sEH) is a key enzyme in the metabolism of epoxy-fatty acids, signaling molecules involved in numerous biologies. Toward finding novel inhibitors of sEH, a library of known drugs was tested for inhibition of sEH. We found that fulvestrant, an anticancer agent, is a potent (KI=26 nM) competitive inhibitor of sEH. From this observation, we found that alkyl-sulfoxides represent a new kind of pharmacophore for the inhibition of sEH.


    Organizational Affiliation

    Department of Entomology and UCD Comprehensive Cancer Center, University of California, One Shields Avenue, Davis, CA 95616, USA. chmorisseau@ucdavis.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional epoxide hydrolase 2A555Homo sapiensMutation(s): 0 
Gene Names: EPHX2
EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (PDB Primary Data)
Find proteins for P34913 (Homo sapiens)
Explore P34913 
Go to UniProtKB:  P34913
NIH Common Fund Data Resources
PHAROS  P34913
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FVS
Query on FVS

Download CCD File 
A
(7beta,9beta,13alpha,17beta)-7-{9-[(R)-(4,4,5,5,5-pentafluoropentyl)sulfinyl]nonyl}estra-1(10),2,4-triene-3,17-diol
C32 H47 F5 O3 S
VWUXBMIQPBEWFH-CIAKRVSBSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FVSKi :  26   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.507α = 90
b = 92.507β = 90
c = 243.811γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2013-06-26
    Changes: Database references