4AOJ

Human TrkA in complex with the inhibitor AZ-23


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIGH AFFINITY NERVE GROWTH FACTOR RECEPTORA, B, C329Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
NIH Common Fund Data Resources
PHAROS:  P04629
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V4Z
Query on V4Z

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
V4ZIC50:  3.200000047683716   nM  BindingDB
V4ZIC50:  9.899999618530273   nM  BindingDB
V4ZIC50:  8.899999618530273   nM  BindingDB
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 = 130.727α = 90
b = 158.419β = 90
c = 152.577γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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