5ALS

ligand complex structure of soluble epoxide hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Successful Generation of Structural Information for Fragment-Based Drug Discovery.

Oster, L.Tapani, S.Xue, Y.Kack, H.

(2015) Drug Discov Today 20: 1104

  • DOI: 10.1016/j.drudis.2015.04.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based drug discovery relies upon structural information for efficient compound progression, yet it is often challenging to generate structures with bound fragments. A summary of recent literature reveals that a wide repertoire of experimenta ...

    Fragment-based drug discovery relies upon structural information for efficient compound progression, yet it is often challenging to generate structures with bound fragments. A summary of recent literature reveals that a wide repertoire of experimental procedures is employed to generate ligand-bound crystal structures successfully. We share in-house experience from setting up and executing fragment crystallography in a project that resulted in 55 complex structures. The ligands span five orders of magnitude in affinity and the resulting structures are made available to be of use, for example, for development of computational methods. Analysis of the results revealed that ligand properties such as potency, ligand efficiency (LE) and, to some degree, clogP influence the success of complex structure generation.


    Organizational Affiliation

    Structure and Biophysics, Discovery Sciences, Innovative Medicines, AstraZeneca R&D, Mölndal, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL EPOXIDE HYDROLASE 2
A
549Homo sapiensMutation(s): 0 
Gene Names: EPHX2
Find proteins for P34913 (Homo sapiens)
Go to Gene View: EPHX2
Go to UniProtKB:  P34913
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
5DQ
Query on 5DQ

Download SDF File 
Download CCD File 
A
N-CYCLOPENTYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-3H-IMIDAZO[4,5-B]PYRIDINE-7-SULFONAMIDE
C18 H17 F3 N4 O2 S
JBHHWVFQIGPHPU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.724α = 90.00
b = 93.724β = 90.00
c = 244.922γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-07-08
    Type: Atomic model, Other
  • Version 1.2: 2015-09-23
    Type: Database references