5KVT | pdb_00005kvt

THE STRUCTURE OF TRKA KINASE DOMAIN BOUND TO THE INHIBITOR ENTRECTINIB

• PDB DOI: https://doi.org/10.2210/pdb5KVT/pdb

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


• Deposited: 2016-07-15 Released: 2017-12-27 
• Deposition Author(s): Jin, L., Yan, S., Wei, G., Li, G., Harris, J., Vernier, J.-M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Antitumor Activity and Safety of the Pan-TRK, ROS1, and ALK inhibitor Entrectinib (RXDX-101): Combined Results from Two Phase I Trials

Drilon, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.16 kDa 
• Atom Count: 2,364 
• Modeled Residue Count: 287 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	293	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YMX	B [auth A]	Entrectinib C31 H34 F2 N6 O2 HAYYBYPASCDWEQ-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YMX	BindingDB:  5KVT	IC50: min: 0.22, max: 400 (nM) from 12 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.9	α = 90
b = 75.9	β = 90
c = 111.74	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Jin, L., Yan, S., Wei, G., Li, G., Harris, J., Vernier, J.-M.

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description