Biological Assembly 1  

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

Global Symmetry: Dihedral - D6  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 112.26 kDa 
• Atom Count: 6412 
• Modelled Residue Count: 779 
• Deposited Residue Count: 987 
• Unique protein chains: 1

4AOJ

Human TrkA in complex with the inhibitor AZ-23

• DOI: 10.2210/pdb4AOJ/pdb

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


• Deposited: 2012-03-28 Released: 2012-08-15 
• Deposition Author(s): Wang, T., Lamb, M.L., Block, M.H., Davies, A.M., Han, Y., Hoffmann, E., Ioannidis, S., Josey, J.A., Liu, Z., Lyne, P.D., MacIntyre, T., Mohr, P.J., Omer, C.A., Sjogren, T., Thress, K., Wang, B., Wang, H., Yu, D., Zhang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.242 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

Literature

Discovery of Disubstituted Imidazo[4,5-B]Pyridines and Purines as Potent Trka Inhibitors

Wang, T., Lamb, M.L., Block, M.H., Davies, A.M., Han, Y., Hoffmann, E., Ioannidis, S., Josey, J.A., Liu, Z., Lyne, P.D., Macintyre, T., Mohr, P.J., Omer, C.A., Sjogren, T., Thress, K., Wang, B., Wang, H., Yu, D., Zhang, H.

(2012) ACS Med Chem Lett 3: 705

• PubMed: 24900538 
• DOI: 10.1021/ml300074j
• Primary Citation of Related Structures:  
  4AOJ


• PubMed Abstract: 
  

Trk receptor tyrosine kinases have been implicated in cancer and pain. A crystal structure of TrkA with AZ-23 (1a) was obtained, and scaffold hopping resulted in two 5/6-bicyclic series comprising either imidazo[4,5-b]pyridines or purines. Further optimization of these two fusion series led to compounds with subnanomolar potencies against TrkA kinase in cellular assays. Antitumor effects in a TrkA-driven mouse allograft model were demonstrated with compounds 2d and 3a.

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Organizational Affiliation: 

Oncology Innovative Medicines Unit, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR	A, B, C	329	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V4Z (Subject of Investigation/LOI)	D [auth A], G [auth B], J [auth C]	5-chloranyl-N2-[(1S)-1-(5-fluoranylpyridin-2-yl)ethyl]-N4-(3-propan-2-yloxy-1H-pyrazol-5-yl)pyrimidine-2,4-diamine C17 H19 Cl F N7 O LBVKEEFIPBQIMD-JTQLQIEISA-N
ZN	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
V4Z	BindingDB:  4AOJ	Ki: min: 0.36, max: 3.7 (nM) from 2 assay(s)
		Kd: 2 (nM) from 1 assay(s)
		IC50: min: 0.3, max: 9.9 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.242 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.727	α = 90
b = 158.419	β = 90
c = 152.577	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-03-28 
• Released Date: 2012-08-15 
Deposition Author(s): Wang, T., Lamb, M.L., Block, M.H., Davies, A.M., Han, Y., Hoffmann, E., Ioannidis, S., Josey, J.A., Liu, Z., Lyne, P.D., MacIntyre, T., Mohr, P.J., Omer, C.A., Sjogren, T., Thress, K., Wang, B., Wang, H., Yu, D., Zhang, H.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other