4Y48

Endothiapepsin in complex with fragment B50


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.249 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

Huschmann, F.U.Linnik, J.Sparta, K.Uhlein, M.Wang, X.Metz, A.Schiebel, J.Heine, A.Klebe, G.Weiss, M.S.Mueller, U.

(2016) Acta Crystallogr.,Sect.F 72: 346-355

  • DOI: 10.1107/S2053230X16004623
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compoun ...

    Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.


    Organizational Affiliation

    Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY

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A
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PRO
Query on PRO

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A
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.249 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.177α = 90.00
b = 73.519β = 109.44
c = 53.097γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BMBFGermany05K13RM1

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references
  • Version 1.2: 2016-05-11
    Type: Database references