4C4X

Crystal structure of human bifunctional epoxide hydroxylase 2 complexed with C9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.4 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:  
    4C4X, 4C4Y, 4C4Z, 4YXR, 4YXS

  • 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). cigr@nmr.mpibpc.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BIFUNCTIONAL EPOXIDE HYDROLASE 2A, B326Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
W9M
Query on W9M

Download CCD File 
A, B
3-(3,4-dichlorophenyl)-1,1-dimethyl-urea
C9 H10 Cl2 N2 O
XMTQQYYKAHVGBJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.69α = 90
b = 79.87β = 89.95
c = 88.61γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-01
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references
  • Version 1.2: 2015-06-10
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation