3PBD

Endothiapepsin in complex with a fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.

Koster, H.Craan, T.Brass, S.Herhaus, C.Zentgraf, M.Neumann, L.Heine, A.Klebe, G.

(2011) J.Med.Chem. 54: 7784-7796

  • DOI: 10.1021/jm200642w
  • Primary Citation of Related Structures:  
  • Also Cited By: 4YCK, 5J25, 5ISK, 5ISJ, 5IS4, 5HCO, 5DR8, 5DR7, 5DR4, 5DR3, 5DR1, 5DR0, 5DQ5, 5DQ4, 5DQ2, 5DQ1, 5DPZ, 4YD7, 4YD6, 4YD5, 4YD4, 4YD3, 4YCY, 4YCT, 4Y5P, 4Y5N, 4Y5M, 4Y5L, 4Y5K, 4Y5G, 4Y5E, 4Y5C, 4Y5B, 4Y5A, 4Y58, 4Y57, 4Y56, 4Y54, 4Y53, 4Y51, 4Y50, 4Y4Z, 4Y4X, 4Y4W, 4Y4U, 4Y4T, 4Y4E, 4Y4C, 4Y4B, 4Y4A, 4Y47, 4Y45, 4Y44, 4Y43, 4Y41, 4Y3Z, 4Y3X, 4Y3W, 4Y3T, 4Y3S, 4Y3R, 4Y3Q, 4Y3P, 4Y3N, 4Y3M, 4Y3L, 4Y3H, 4Y3G, 4Y3F, 4Y3E, 4Y3D, 4Y3A, 4Y39, 4Y37, 4Y36, 4Y35

  • PubMed Abstract: 
  • Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for comme ...

    Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Philipps University 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F05
Query on F05

Download SDF File 
Download CCD File 
A
2H-isoindol-1-amine
C8 H8 N2
SPSYMWKHDUJABD-UHFFFAOYSA-N
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.330α = 90.00
b = 73.110β = 109.75
c = 52.730γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SHELXL-97refinement
HKL-2000data scaling
HKL-2000data reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-11-02
    Type: Database references
  • Version 1.2: 2011-11-30
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection