5OJE

Endothiapepsin with Ligand VSK-B24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.579 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.1 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


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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A
(2~{S})-2-azanyl-3-(1~{H}-indol-3-yl)-~{N}-[2-(2,4,6-trimethylphenyl)ethyl]propanamide
VSK-B24
C22 H27 N3 O
BQKLGIPTHQLBPK-FQEVSTJZSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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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: 1.579 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.404α = 90.00
b = 73.009β = 110.06
c = 53.069γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSapp 2.0data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references