2VIV

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator.

Frederickson, M.Callaghan, O.Chessari, G.Congreve, M.Cowan, S.R.Matthews, J.E.Mcmenamin, R.Smith, D.Vinkovic, M.Wallis, N.G.

(2008) J.Med.Chem. 51: 183

  • DOI: 10.1021/jm701359z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based lead discovery has been applied to urokinase-type plasminogen activator (uPA). The (R)-enantiomer of the orally active drug mexiletine 5 (a fragment hit from X-ray crystallographic screening) was the chemical starting point. Structure- ...

    Fragment-based lead discovery has been applied to urokinase-type plasminogen activator (uPA). The (R)-enantiomer of the orally active drug mexiletine 5 (a fragment hit from X-ray crystallographic screening) was the chemical starting point. Structure-aided design led to elaborated inhibitors that retained the key interactions of (R)-5 while gaining extra potency by simultaneously occupying neighboring regions of the active site. Subsequent optimization led to 15, a potent, selective, and orally bioavailable inhibitor of uPA.


    Organizational Affiliation

    Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom. m.frederickson@astex-therapeutics.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B
A
253Homo sapiensMutation(s): 2 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to Gene View: PLAU
Go to UniProtKB:  P00749
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
VG2
Query on VG2

Download SDF File 
Download CCD File 
A
4-(2-aminoethoxy)-N-(3-chloro-5-piperidin-1-ylphenyl)-3,5-dimethylbenzamide
C22 H28 Cl N3 O2
JDYIYIRPQKMWMM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VG2IC50: 520 nM (99) BINDINGDB
VG2IC50: 520 nM BINDINGMOAD
VG2IC50: 520 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.338α = 90.00
b = 54.001β = 90.00
c = 81.938γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection