6PMB

TRK-A IN COMPLEX WITH LIGAND 1a

• PDB DOI: https://doi.org/10.2210/pdb6PMB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-01 Released: 2020-02-26 
• Deposition Author(s): Subramanian, G., Brown, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.214 
• R-Value Observed: 0.219 

Literature

Synthetic inhibitor leads of human tropomyosin receptor kinase A ( h TrkA).

Subramanian, G., Vairagoundar, R., Bowen, S.J., Roush, N., Zachary, T., Javens, C., Williams, T., Janssen, A., Gonzales, A.

(2020) RSC Med Chem 11: 370-377

• PubMed: 33479642 
• DOI: https://doi.org/10.1039/c9md00554d
• Primary Citation of Related Structures:  
  6PMA, 6PMB, 6PMC, 6PME


• PubMed Abstract: 
  

  In silico virtual screening followed by in vitro biochemical, biophysical, and cellular screening resulted in the identification of distinctly different h TrkA kinase domain inhibitor scaffolds. X-ray structural analysis of representative inhibitors bound to h TrkA kinase domain defined the binding mode and rationalized the mechanism of action. Preliminary assessment of the sub-type selectivity against the closest h TrkB isoform, and early ADME guided the progression of select inhibitor leads in the screening cascade. The possibility of the actives sustaining to known h TrkA resistance mutations assessed in silico offers initial guidance into the required multiparametric lead optimization to arrive at a clinical candidate.

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Organizational Affiliation: 

Veterinary Medicine Research & Development , Zoetis , 333 Portage Street , Kalamazoo , MI 49007 , USA . Email: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 35.78 kDa 
• Atom Count: 2,363 
• Modelled Residue Count: 288 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	311	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 GTEx:  ENSG00000198400

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OQM (Subject of Investigation/LOI)	B [auth A]	2-[5,7-dimethyl-2-(pyridin-3-yl)[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]-N-[3-(trifluoromethyl)phenyl]acetamide C21 H17 F3 N6 O MTJCWZPTCSKXKK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.282 
• R-Value Work: 0.214 
• R-Value Observed: 0.219 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.109	α = 90
b = 52.109	β = 90
c = 226.747	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Subramanian, G., Brown, D.G.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2024-03-13
  Changes: Advisory, Data collection, Database references