6PMA

TRK-A IN COMPLEX WITH LIGAND

• PDB DOI: https://doi.org/10.2210/pdb6PMA/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: 2.53 Å
• R-Value Free: 
  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

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: 35.91 kDa 
• Atom Count: 2,381 
• Modelled Residue Count: 290 
• 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
OQS (Subject of Investigation/LOI)	B [auth A]	N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[1-(4-methoxyphenyl)-4-oxo-1,4-dihydro-5H-pyrazolo[3,4-d]pyrimidin-5-yl]acetamide C21 H15 Cl F3 N5 O3 VVMPLFOVCSRJQQ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
OQS	BindingDB:  6PMA	IC50: min: 102, max: 7500 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.266 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.094	α = 90
b = 52.094	β = 90
c = 227.16	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	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: 2024-11-13
  Changes: Advisory, Data collection, Database references, Structure summary