Pyrrolidine fragment 5b bound to endothiapepsin

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 

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Fragtory: Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp 3 -Enriched Fragment Library.

Buhrmann, M.Kallepu, S.Warmuth, J.D.Wiese, J.N.Ehrt, C.Vatheuer, H.Hiller, W.Seitz, C.Levy, L.Czodrowski, P.Sievers, S.Muller, M.P.Rauh, D.

(2023) J Med Chem 66: 6297-6314

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00187
  • Primary Citation of Related Structures:  
    8C6P, 8C6Q, 8C6S, 8C6T, 8C70, 8C71, 8C72, 8C74

  • PubMed Abstract: 

    Fragment-based drug discovery has played an important role in medicinal chemistry and pharmaceutical research. Despite numerous demonstrated successes, the limited diversity and overrepresentation of planar, sp 2 -rich structures in commercial libraries often hamper the full potential of this approach. Hence, the thorough design of screening libraries inevitably determines the probability for meaningful hits and subsequent structural elaboration. Against this background, we present the generation of an exclusive fragment library based on iterative entry nomination by a specifically designed computational workflow: "Fragtory". Following a pharmacophore diversity-driven approach, we used Fragtory in an interdisciplinary academic setting to guide both tailored synthesis efforts and the implementation of in-house compounds to build a curated 288-member library of sp 3 -enriched fragments. Subsequent NMR screens against a model protein and hit validation by protein crystallography led to the identification of structurally novel ligands that were further characterized by isothermal titration calorimetry, demonstrating the applicability of our experimental approach.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endothiapepsin419Cryphonectria parasiticaMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TVO (Subject of Investigation/LOI)
Query on TVO

Download Ideal Coordinates CCD File 
C [auth A](3~{R},4~{R})-4-(3,4-dihydro-1~{H}-isoquinolin-2-yl)pyrrolidin-3-ol
C13 H18 N2 O
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.61α = 90
b = 73.77β = 110.16
c = 53.45γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyINST 212/474-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release