4C4Y

Crystal structure of human bifunctional epoxide hydroxylase 2 complexed with A4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles.

Pilger, J.Mazur, A.Monecke, P.Schreuder, H.Elshorst, B.Bartoschek, S.Langer, T.Schiffer, A.Krimm, I.Wegstroth, M.Lee, D.Hessler, G.Wendt, K.Becker, S.Griesinger, C.

(2015) Angew.Chem.Int.Ed.Engl. 54: 6511

  • DOI: 10.1002/anie.201500671
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structure-based drug design (SBDD) is a powerful and widely used approach to optimize affinity of drug candidates. With the recently introduced INPHARMA method, the binding mode of small molecules to their protein target can be characterized even if ...

    Structure-based drug design (SBDD) is a powerful and widely used approach to optimize affinity of drug candidates. With the recently introduced INPHARMA method, the binding mode of small molecules to their protein target can be characterized even if no spectroscopic information about the protein is known. Here, we show that the combination of the spin-diffusion-based NMR methods INPHARMA, trNOE, and STD results in an accurate scoring function for docking modes and therefore determination of protein-ligand complex structures. Applications are shown on the model system protein kinase A and the drug targets glycogen phosphorylase and soluble epoxide hydrolase (sEH). Multiplexing of several ligands improves the reliability of the scoring function further. The new score allows in the case of sEH detecting two binding modes of the ligand in its binding site, which was corroborated by X-ray analysis.


    Organizational Affiliation

    Abteilung für NMR-basierte Strukturbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Germany).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL EPOXIDE HYDROLASE 2
A
326Homo sapiensMutation(s): 0 
Gene Names: EPHX2
Find proteins for P34913 (Homo sapiens)
Go to Gene View: EPHX2
Go to UniProtKB:  P34913
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7WI
Query on 7WI

Download SDF File 
Download CCD File 
A
1-(3-chlorophenyl)-3-(2-methoxyethyl)urea
C10 H13 Cl N2 O2
OCWOGWHGSTYVMJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.258 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.640α = 90.00
b = 46.340β = 90.00
c = 80.290γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2015-06-10
    Type: Database references