6J5L | pdb_00006j5l

Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 10e


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B9CClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

The discovery of novel 3-aryl-indazole derivatives as peripherally restricted pan-Trk inhibitors for the treatment of pain.

Shirahashi, H.Toriihara, E.Suenaga, Y.Yoshida, H.Akaogi, K.Endou, Y.Wakabayashi, M.Takashima, M.

(2019) Bioorg Med Chem Lett 29: 2320-2326

  • DOI: https://doi.org/10.1016/j.bmcl.2019.06.018
  • Primary Citation of Related Structures:  
    6J5L

  • PubMed Abstract: 

    The design, synthesis, and biological evaluation of novel 3-aryl-indazole derivatives as peripherally selective pan-Trk inhibitors are described. Three strategies were used to obtain a potent compound exhibiting low central nervous system (CNS) penetration and high plasma exposure: 1) a structure-based drug design (SBDD) approach was used to improve potency; 2) a substrate for an efflux transporter for lowering brain penetration was explored; and 3) the most basic pKa (pKa-MB) value was used as an indicator to identify compounds with good membrane permeability. This enabled the identification of the peripherally targeted 17c with the potency, kinase-selectivity, and plasma exposure required to demonstrate in vivo efficacy in a Complete Freund's adjuvant (CFA)-induced thermal hypersensitivity model.


  • Organizational Affiliation

    Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan. Electronic address: shirahashi.hd@om.asahi-kasei.co.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor303Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B9C (Subject of Investigation/LOI)
Query on B9C

Download Ideal Coordinates CCD File 
B [auth A]N-{2-[({3-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indazol-5-yl}amino)methyl]phenyl}methanesulfonamide
C24 H27 N7 O2 S
ZTJQDVXGJTWIGK-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
B9C BindingDB:  6J5L IC50: min: 1.6, max: 27 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.193α = 90
b = 104.193β = 90
c = 203.838γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted B9CClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description