4X3J

Selection of fragments for kinase inhibitor design: decoration is key


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selection of fragments for kinase inhibitor design: decoration is key.

Czodrowski, P.Holzemann, G.Barnickel, G.Greiner, H.Musil, D.

(2015) J.Med.Chem. 58: 457-465

  • DOI: 10.1021/jm501597j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In fragment-based screening, the choice of the best suited fragment hit among the detected hits is crucial for success. In our study, a kinase lead compound was fragmented, the hinge-binding motif extracted as a core fragment, and a minilibrary of fi ...

    In fragment-based screening, the choice of the best suited fragment hit among the detected hits is crucial for success. In our study, a kinase lead compound was fragmented, the hinge-binding motif extracted as a core fragment, and a minilibrary of five similar compounds with fragment-like properties was selected from our proprietary compound database. The structures of five fragments in complex with transforming growth factor β receptor type 1 kinase domain were determined by X-ray crystallography. Three different binding modes of the fragments are observed that depend on the position and the type of the substitution at the core fragment. The influence of different substituents on the preferred fragment pose was analyzed by various computational approaches. We postulate that the replacement of water molecules leads to the different binding modes.


    Organizational Affiliation

    Discovery Technologies, Merck Serono Research, Merck Serono R&D, Merck KGaA , Frankfurter Strasse 250, 64293 Darmstadt, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Angiopoietin-1 receptor
A
321Homo sapiensMutation(s): 1 
Gene Names: TEK (TIE2, VMCM, VMCM1)
EC: 2.7.10.1
Find proteins for Q02763 (Homo sapiens)
Go to Gene View: TEK
Go to UniProtKB:  Q02763
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3WR
Query on 3WR

Download SDF File 
Download CCD File 
A
1-[4-(4-amino-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl)phenyl]-3-[2-fluoro-5-(trifluoromethyl)phenyl]urea
C21 H14 F4 N6 O2
OWKPAZCWJGPSQU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.255 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.456α = 90.00
b = 62.456β = 90.00
c = 178.450γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Database references