4AT5

CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Crystal Structures of Trka and Trkb Suggest Key Regions for Achieving Selective Inhibition.

Bertrand, T.Kothe, M.Liu, J.Dupuy, A.Rak, A.Berne, P.F.Davis, S.Gladysheva, T.Valtre, C.Crenne, J.Y.Mathieu, M.

(2012) J Mol Biol 423: 439

  • DOI: 10.1016/j.jmb.2012.08.002
  • Primary Citation of Related Structures:  
    4F0I, 4ASZ, 4AT3, 4AT4, 4AT5

  • PubMed Abstract: 
  • The Trk family of neurotrophin receptors, which includes the three highly homologous proteins TrkA, TrkB and TrkC, is strongly associated with central and peripheral nervous system processes. Trk proteins are also of interest in oncology, since Trk activ ...

    The Trk family of neurotrophin receptors, which includes the three highly homologous proteins TrkA, TrkB and TrkC, is strongly associated with central and peripheral nervous system processes. Trk proteins are also of interest in oncology, since Trk activation has been observed in several cancer types. While Trk kinases are attractive oncology targets, selectivity might be more of an issue than for other kinases due to potential CNS side effects if several Trk kinases are simultaneously targeted. In order to address this issue, we present here the first structures of human TrkA and TrkB kinase domains and three complexes between TrkB and Trk inhibitors. These structures reveal different conformations of the kinase domain and suggest new regions of selectivity among the Trk family.


    Organizational Affiliation

    Department of Structure, Design, and Informatics, Sanofi, 13 Quai Jules Guesde, Vitry-sur-Seine, 94403 Cedex, France. thomas.bertrand@sanofi.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BDNF/NT-3 GROWTH FACTORS RECEPTOR A299Homo sapiensMutation(s): 0 
Gene Names: NTRK2TRKB
EC: 2.7.10.1
Find proteins for Q16620 (Homo sapiens)
Explore Q16620 
Go to UniProtKB:  Q16620
NIH Common Fund Data Resources
PHAROS:  Q16620
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MUJ
Query on MUJ

Download Ideal Coordinates CCD File 
A
5-{3-methoxy-4-[(4-methoxybenzyl)oxy]benzyl}pyrimidine-2,4-diamine
C20 H22 N4 O3
MYQAUKPBNJWPIE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MUJKd:  36   nM  BindingDB
MUJIC50 :  38   nM  PDBBind
MUJIC50:  38   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.54α = 90
b = 94.19β = 90
c = 46.32γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Refinement description
  • Version 1.3: 2019-04-03
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-04-24
    Changes: Data collection, Source and taxonomy