5H3Q

Crystal Structure of TrkA kinase with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.bmcl.2017.01.056
  • Primary Citation of Related Structures:  
    5H3Q

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor324Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
PHAROS:  P04629
GTEx:  ENSG00000198400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7HF
Query on 7HF

Download Ideal Coordinates CCD File 
B [auth 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
DTT
Query on DTT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7HF BindingDB:  5H3Q IC50: min: 2.7, max: 100 (nM) from 3 assay(s)
Binding MOAD:  5H3Q IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.845α = 90
b = 157.195β = 90
c = 52.306γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description