Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37252.39 
• Atom Count: 1919 
• Residue Count: 321 
• Unique protein chains: 1

4X3J

Selection of fragments for kinase inhibitor design: decoration is key

• DOI: 10.2210/pdb4X3J/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): 1 


• Deposited: 2014-11-30 Released: 2014-12-24 
• Deposition Author(s): Czodrowski, P., Hoelzemann, G., Barnickel, G., Greiner, H., Musil, D.

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Experimental Data Snapshot

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

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

• PubMed: 25437144 
• DOI: 10.1021/jm501597j
• Primary Citation of Related Structures:  
  4X2N, 4X2K, 4X2J, 4X2G, 4X2F, 4X0M


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Angiopoietin-1 receptor	A	321	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
3WR	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

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 = 62.456	α = 90.00
b = 62.456	β = 90.00
c = 178.450	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-30 
• Released Date: 2014-12-24 
• Deposition Author(s): Czodrowski, P., Hoelzemann, G., Barnickel, G., Greiner, H., Musil, D.

Revision History 

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