5OJE | pdb_00005oje

Endothiapepsin with Ligand VSK-B24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design and Synthesis of Bioisosteres of Acylhydrazones as Stable Inhibitors of the Aspartic Protease Endothiapepsin.

Jumde, V.R.Mondal, M.Gierse, R.M.Unver, M.Y.Magari, F.van Lier, R.C.W.Heine, A.Klebe, G.Hirsch, A.K.H.

(2018) ChemMedChem 13: 2266-2270

  • DOI: https://doi.org/10.1002/cmdc.201800446
  • Primary Citation Related Structures: 
    5OJE

  • PubMed Abstract: 

    Acylhydrazone-based dynamic combinatorial chemistry (DCC) is a powerful strategy for the rapid identification of novel hits. Even though acylhydrazones are important structural motifs in medicinal chemistry, their further progression in development may be hampered by major instability and potential toxicity under physiological conditions. It is therefore of paramount importance to identify stable replacements for acylhydrazone linkers. Herein, we present the first report on the design and synthesis of stable bioisosteres of acylhydrazone-based inhibitors of the aspartic protease endothiapepsin as a follow-up to a DCC study. The most successful bioisostere is equipotent, bears an amide linker, and we confirmed its binding mode by X-ray crystallography. Having some validated bioisosteres of acylhydrazones readily available might accelerate hit-to-lead optimization in future acylhydrazone-based DCC projects.


  • Organizational Affiliation
    • Chemical Biology, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 34.58 kDa 
  • Atom Count: 2,912 
  • Modeled Residue Count: 330 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VSK
(Subject of Investigation/LOI)

Query on VSK



Download:Ideal Coordinates CCD File
B [auth A](2~{S})-2-azanyl-3-(1~{H}-indol-3-yl)-~{N}-[2-(2,4,6-trimethylphenyl)ethyl]propanamide
C22 H27 N3 O
BQKLGIPTHQLBPK-FQEVSTJZSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
D [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.404α = 90
b = 73.009β = 110.06
c = 53.069γ = 90
Software Package:
Software NamePurpose
XDSapp 2.0data reduction
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary