5AK6

ligand complex structure of soluble epoxide hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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. Electronic address: helena.kack@astrazeneca.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BIFUNCTIONAL EPOXIDE HYDROLASE 2
A
549HOMO 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)
Go to UniProtKB:  P34913
NIH Common Fund Data Resources
PHAROS  P34913
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YPN
Query on YPN

Download CCD File 
A
2-[(5-CHLORO-2-PYRIDYL)SULFANYL]ETHANOL
C7 H8 Cl N O S
KLOJLJIHCJJDCT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YPNIC50:  362400   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.738α = 90
b = 91.738β = 90
c = 245.273γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other