ligand complex structure of soluble epoxide hydrolase

Experimental Data Snapshot

  • Resolution: 2.57 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.drudis.2015.04.005
  • Primary Citation of Related Structures:  
    5AHX, 5AI0, 5AI4, 5AI5, 5AI6, 5AI8, 5AI9, 5AIA, 5AIB, 5AIC, 5AK3, 5AK4, 5AK5, 5AK6, 5AKE, 5AKG, 5AKH, 5AKI, 5AKJ, 5AKK, 5AKL, 5AKX, 5AKY, 5AKZ, 5ALD, 5ALE, 5ALF, 5ALG, 5ALH, 5ALI, 5ALJ, 5ALK, 5ALL, 5ALM, 5ALN, 5ALO, 5ALP, 5ALQ, 5ALR, 5ALS, 5ALT, 5ALU, 5ALV, 5ALW, 5ALX, 5ALY, 5ALZ, 5AM0, 5AM1, 5AM2

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BIFUNCTIONAL EPOXIDE HYDROLASE 2549Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34913
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.57 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.724α = 90
b = 93.724β = 90
c = 244.922γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Atomic model, Other
  • Version 1.2: 2015-09-23
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description