4LHH

Endothiapepsin in complex with 2mM acylhydrazone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry.

Mondal, M.Radeva, N.Koster, H.Park, A.Potamitis, C.Zervou, M.Klebe, G.Hirsch, A.K.

(2014) Angew.Chem.Int.Ed.Engl. 53: 3259-3263

  • DOI: 10.1002/anie.201309682
  • Primary Citation of Related Structures:  
  • Also Cited By: 5HCT

  • PubMed Abstract: 
  • Structure-based design (SBD) can be used for the design and/or optimization of new inhibitors for a biological target. Whereas de novo SBD is rarely used, most reports on SBD are dealing with the optimization of an initial hit. Dynamic combinatorial ...

    Structure-based design (SBD) can be used for the design and/or optimization of new inhibitors for a biological target. Whereas de novo SBD is rarely used, most reports on SBD are dealing with the optimization of an initial hit. Dynamic combinatorial chemistry (DCC) has emerged as a powerful strategy to identify bioactive ligands given that it enables the target to direct the synthesis of its strongest binder. We have designed a library of potential inhibitors (acylhydrazones) generated from five aldehydes and five hydrazides and used DCC to identify the best binder(s). After addition of the aspartic protease endothiapepsin, we characterized the protein-bound library member(s) by saturation-transfer difference NMR spectroscopy. Cocrystallization experiments validated the predicted binding mode of the two most potent inhibitors, thus demonstrating that the combination of deā€…novo SBD and DCC constitutes an efficient starting point for hit identification and optimization.


    Organizational Affiliation

    Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen (The Netherlands) http://www.rug.nl/research/bio-organic-chemistry/hirsch/




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
1TZ
Query on 1TZ

Download SDF File 
Download CCD File 
A
(2S)-2-azanyl-3-(3H-indol-3-yl)-N-[(E)-(2,4,6-trimethylphenyl)methylideneamino]propanamide
(2S)-2-amino-3-(1H-indol-3-yl)-N-[(E)-(2,4,6-trimethylphenyl)methyleneamino]propanamide
C21 H24 N4 O
KKEDWXLWEPQNQM-OGBFJMLUSA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1TZKi: 6000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.467α = 90.00
b = 73.104β = 109.61
c = 53.134γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MAR345dtbdata collection
PHENIXrefinement
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release