5H3Q

Crystal Structure of TrkA kinase with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The juxtamembrane region of TrkA kinase is critical for inhibitor selectivity

Furuya, N.Momose, T.Katsuno, K.Fushimi, N.Muranaka, H.Handa, C.Ozawa, T.Kinoshita, T.

(2017) Bioorg. Med. Chem. Lett. 27: 1233-1236

  • DOI: 10.1016/j.bmcl.2017.01.056

  • PubMed Abstract: 
  • Although numerous crystal structures for protein kinases have been reported, many include only the kinase domain but not the juxtamembrane (JM) region, a critical activity-controlling segment of receptor tyrosine kinases (RTKs). In this study, we det ...

    Although numerous crystal structures for protein kinases have been reported, many include only the kinase domain but not the juxtamembrane (JM) region, a critical activity-controlling segment of receptor tyrosine kinases (RTKs). In this study, we determined the X-ray crystal structure of the tropomyosin receptor kinase (Trk) A selective inhibitor A1 complexed with the TrkA kinase domain and the JM region. This structure revealed that the unique inhibitor-binding pocket created by a novel JM configuration yields significant potency and high selectivity against TrkB and TrkC. Moreover, we validated the importance of the JM region for the potency of A1 using in vitro assays. The introduction of moieties that interact with the JM region will be one of the most effective strategies for producing highly selective RTK inhibitors.


    Organizational Affiliation

    Kissei Pharmaceutical, 4365-1, Kashiwabara, Hotaka, Azumino City, Nagano Pref. 399-8304, Japan; Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: noritaka_furuya@pharm.kissei.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity nerve growth factor receptor
A
324Homo sapiensMutation(s): 0 
Gene Names: NTRK1 (MTC, TRK, TRKA)
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Go to Gene View: NTRK1
Go to UniProtKB:  P04629
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
7HF
Query on 7HF

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Download CCD File 
A
1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea
C26 H31 F2 N5 O3
SQGLEZDWHPDRDX-NZQKXSOJSA-N
 Ligand Interaction
DTT
Query on DTT

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Download CCD File 
A
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 140.845α = 90.00
b = 157.195β = 90.00
c = 52.306γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-10-26 
  • Released Date: 2017-02-22 
  • Deposition Author(s): Noritaka, F.

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references