3FCQ

Thermolysin inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fragment-Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition.

Englert, L.Silber, K.Steuber, H.Brass, S.Over, B.Gerber, H.D.Heine, A.Diederich, W.E.Klebe, G.

(2010) Chemmedchem 5: 930-940

  • DOI: 10.1002/cmdc.201000084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based drug discovery has gained a foothold in today's lead identification processes. We present the application of in silico fragment-based screening for the discovery of novel lead compounds for the metalloendoproteinase thermolysin. We hav ...

    Fragment-based drug discovery has gained a foothold in today's lead identification processes. We present the application of in silico fragment-based screening for the discovery of novel lead compounds for the metalloendoproteinase thermolysin. We have chosen thermolysin to validate our screening approach as it is a well-studied enzyme and serves as a model system for other proteases. A protein-targeted virtual library was designed and screening was carried out using the program AutoDock. Two fragment hits could be identified. For one of them, the crystal structure in complex with thermolysin is presented. This compound was selected for structure-based optimization of binding affinity and improvement of ligand efficiency, while concomitantly keeping the fragment-like properties of the initial hit. Redesigning the zinc coordination group revealed a novel class of fragments possessing K(i) values as low as 128 microM, thus they provide a good starting point for further hit evolution in a tailored lead design.


    Organizational Affiliation

    Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
M3S
Query on M3S

Download SDF File 
Download CCD File 
A
2-(acetyloxy)-3-methylbenzoic acid
C10 H10 O4
XRBMKGUDDJPAMH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M3SKi: 1700000 nM BINDINGMOAD
M3SKi: 1700000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.176 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.718α = 90.00
b = 92.718β = 90.00
c = 129.965γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
MAR345dtbdata collection
HKL-2000data reduction
CNSrefinement
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-07-24
    Type: Data collection, Refinement description