5LWU

Structure resulting from an endothiapepsin crystal soaked with a dimeric derivative of fragment 177


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.109 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring.

Cramer, J.Schiebel, J.Wulsdorf, T.Grohe, K.Najbauer, E.E.Ehrmann, F.R.Radeva, N.Zitzer, N.Linne, U.Linser, R.Heine, A.Klebe, G.

(2017) Angew. Chem. Int. Ed. Engl. 56: 1908-1913

  • DOI: 10.1002/anie.201609824
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening ...

    With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced-fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false-positive hit.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothiapepsin
A
330Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPA (EPN-1)
EC: 3.4.23.22
Find proteins for P11838 (Cryphonectria parasitica)
Go to UniProtKB:  P11838
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TFA
Query on TFA

Download SDF File 
Download CCD File 
A
trifluoroacetic acid
C2 H F3 O2
DTQVDTLACAAQTR-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.109 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.325α = 90.00
b = 73.340β = 109.86
c = 53.063γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BMBFGermany05K13RM1

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release