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 1.4 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BIFUNCTIONAL EPOXIDE HYDROLASE 2549Homo sapiensMutation(s): 0 
EC: 3.3.2.10 (PDB Primary Data), 3.1.3.76 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YPN
Query on YPN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
2-[(5-CHLORO-2-PYRIDYL)SULFANYL]ETHANOL
C7 H8 Cl N O S
KLOJLJIHCJJDCT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
YPN Binding MOAD:  5AK6 IC50: 3.26e+5 (nM) from 1 assay(s)
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  (Full details and data files)

  • 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
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description