7IFQ | pdb_00007ifq

Endothiapepsin crystal A05a from ECBL-96 fragment library screening campaign used for PanDDA ground state calculation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

From fragments to follow-ups: rapid hit expansion by making use of EU-OPENSCREEN resources.

Benz, L.S.Wollenhaupt, J.Jirgensons, A.Miletic, T.Mueller, U.Weiss, M.S.

(2025) RSC Med Chem 

  • DOI: https://doi.org/10.1039/d5md00684h
  • Primary Citation of Related Structures:  
    7IEP, 7IEQ, 7IER, 7IES, 7IET, 7IEU, 7IEV, 7IEW, 7IEX, 7IEY, 7IEZ, 7IF0, 7IF1, 7IF2, 7IF3, 7IF4, 7IF5, 7IF6, 7IF7, 7IF8, 7IF9, 7IFA, 7IFB, 7IFC, 7IFD, 7IFE, 7IFF, 7IFG, 7IFH, 7IFI, 7IFJ, 7IFK, 7IFL, 7IFM, 7IFN, 7IFO, 7IFP, 7IFQ, 7IFR, 7IFS, 7IFT, 7IFU, 7IFV, 7IFW, 7IFX, 7IFY, 7IFZ, 7IG0, 7IG1, 7IG2

  • PubMed Abstract: 

    Quite frequently, it is the progression of initial crystallographic fragment screening hits into more potent binders to their target, which constitutes the major bottleneck in many academic compound or drug development projects. While high quality starting points are critical to the success of a drug development project, it is equally important to have accessible pathways for further compound development. Here, we present two crystallographic fragment screening campaigns using a 96 fragment sub-selection of the European Fragment Screening Library (EFSL) provided by EU-OPENSCREEN. The two campaigns against the targets endothiapepsin and the NS2B-NS3 Zika protease, yielded hit rates of 31% and 18%, respectively. Further, we present how within the framework of the EU-OPENSCREEN European Research Infrastructure Consortium (ERIC) fast identification of follow-up compounds can be realized. With just one round of testing related compounds from the European Chemical Biology Library, two follow-up binders for each of the two targets could be identified proving the feasibility of this approach.


  • Organizational Affiliation
    • Macromolecular Crystallography, Helmholtz-Zentrum Berlin Albert-Einstein-Str. 15 12489 Berlin Germany manfred.weiss@helmholtz-berlin.de.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endothiapepsin330Cryphonectria parasiticaMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.39α = 90
b = 73.57β = 109.35
c = 52.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionEuropean Union871037

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release