Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.74 kDa 
• Atom Count: 2220 
• Modelled Residue Count: 282 
• Deposited Residue Count: 303 
• Unique protein chains: 1

6J5L

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

• PDB DOI: 10.2210/pdb6J5L/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-01-11 Released: 2019-07-17 
• Deposition Author(s): Kensuke, A., Kazutaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

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

• PubMed: 31235262 
• DOI: 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.

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Organizational Affiliation: 

Pharmaceuticals Research Center, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	303	Homo sapiens	Mutation(s): 0  Gene Names: NTRK1, MTC, TRK, TRKA 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B9C (Subject of Investigation/LOI)	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
ID	Source	Binding Affinity
B9C	Binding MOAD:  6J5L	IC50: 1.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.193	α = 90
b = 104.193	β = 90
c = 203.838	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-01-11 
• Released Date: 2019-07-17 
Deposition Author(s): Kensuke, A., Kazutaka, I.

Revision History  

• 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