4AT3

CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH CPD5N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 a ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BDNF/NT-3 GROWTH FACTORS RECEPTOR
A
299Homo sapiensMutation(s): 0 
Gene Names: NTRK2 (TRKB)
EC: 2.7.10.1
Find proteins for Q16620 (Homo sapiens)
Go to Gene View: NTRK2
Go to UniProtKB:  Q16620
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LTI
Query on LTI

Download SDF File 
Download CCD File 
A
(5Z)-5-(carbamoylimino)-3-[(5R)-6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-ylsulfanyl]-2,5-dihydroisothiazole-4-carboxamide
C16 H18 N4 O2 S2
BLCWVDAFBKECPI-PFMFLNCGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LTIIC50: 4 nM BINDINGMOAD
LTIIC50: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.331α = 90.00
b = 94.340β = 90.00
c = 46.037γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
BUSTERrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-10-10
    Type: Database references