5P8R

Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 360


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.

Schiebel, J.Krimmer, S.G.Rower, K.Knorlein, A.Wang, X.Park, A.Y.Stieler, M.Ehrmann, F.R.Fu, K.Radeva, N.Krug, M.Huschmann, F.U.Glockner, S.Weiss, M.S.Mueller, U.Klebe, G.Heine, A.

(2016) Structure 24: 1398-1409

  • DOI: 10.1016/j.str.2016.06.010
  • Primary Citation of Related Structures:  
    5OYQ, 5OYR, 5OYS, 5OYT, 5OYU, 5OYV, 5OYW, 5OYX, 5OYY, 5OYZ, 5OZ0, 5OZ1, 5OZ2, 5OZ3, 5OZ4, 5OZ5, 5OZ6, 5OZ7, 5OZ8, 5OZ9, 5OZA, 5OZB, 5OZC, 5OZD, 5OZE, 5OZF, 5OZG, 5OZH, 5OZI, 5OZJ, 5OZK, 5OZL, 5OZM, 5OZN, 5OZO, 5OZP, 5OZQ, 5OZR, 5OZS, 5OZT, 5OZU, 5OZV, 5OZW, 5OZX, 5OZY, 5OZZ, 5P00, 5P01, 5P02, 5P03

  • PubMed Abstract: 
  • Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design ...

    Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that ∼25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.


    Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany. Electronic address: heinea@mailer.uni-marburg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
endothiapepsinA330Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPAEPN-1
EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica)
Explore P11838 
Go to UniProtKB:  P11838
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11838
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.347α = 90
b = 73.053β = 109.6
c = 52.921γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2017-01-11
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Structure summary
  • Version 1.4: 2021-11-17
    Changes: Data collection, Database references, Structure summary