6PL4

TRK-A IN COMPLEX WITH LIGAND 1

• PDB DOI: https://doi.org/10.2210/pdb6PL4/pdb

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


• Deposited: 2019-06-30 Released: 2020-07-01 
• Deposition Author(s): Subramanian, G., Brown, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.239 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

In Pursuit of an Allosteric Human Tropomyosin Kinase A (hTrkA) Inhibitor for Chronic Pain

Subramanian, G., Duclos, B., Johnson, P.D., Williams, T., Ross, J.T., Bowen, S.J., Zhu, Y., White, J.A., Hedke, C., Huczek, D., Collard, W., Javens, C., Vairagoundar, R., Respondek, T., Zachary, T., Maddux, T., Cox, M.R., Kamerling, S., Gonzales, A.J.

(2021) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.1c00483

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: homology

Macromolecule Content

• Total Structure Weight: 35.91 kDa 
• Atom Count: 2,570 
• Modelled Residue Count: 299 
• 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
OO7 (Subject of Investigation/LOI)	B [auth A]	N-{[5-(methoxymethyl)-2-(trifluoromethoxy)phenyl]methyl}-N'-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)urea C24 H22 F3 N5 O3 KNZNJSNITSGMNY-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
OO7	BindingDB:  6PL4	IC50: min: 3.9, max: 11 (nM) from 3 assay(s)
		EC50: min: 61, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.239 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.052	α = 90
b = 52.052	β = 90
c = 227.917	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Subramanian, G., Brown, D.G.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2021-11-03
  Changes: Advisory, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary