5U6B

Structure of the Axl kinase domain in complex with a macrocyclic inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Axl kinase domain in complex with a macrocyclic inhibitor offers first structural insights into an active TAM receptor kinase.

Gajiwala, K.S.Grodsky, N.Bolanos, B.Feng, J.Ferre, R.Timofeevski, S.Xu, M.Murray, B.W.Johnson, T.W.Stewart, A.

(2017) J. Biol. Chem. 292: 15705-15716

  • DOI: 10.1074/jbc.M116.771485
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The receptor tyrosine kinase family consisting of Tyro3, Axl, and Mer (TAM) is one of the most recently identified receptor tyrosine kinase families. TAM receptors are up-regulated postnatally and maintained at high levels in adults. They all play an ...

    The receptor tyrosine kinase family consisting of Tyro3, Axl, and Mer (TAM) is one of the most recently identified receptor tyrosine kinase families. TAM receptors are up-regulated postnatally and maintained at high levels in adults. They all play an important role in immunity, but Axl has also been implicated in cancer and therefore is a target in the discovery and development of novel therapeutics. However, of the three members of the TAM family, the Axl kinase domain is the only one that has so far eluded structure determination. To this end, using differential scanning fluorimetry and hydrogen-deuterium exchange mass spectrometry, we show here that a lower stability and greater dynamic nature of the Axl kinase domain may account for its poor crystallizability. We present the first structural characterization of the Axl kinase domain in complex with a small-molecule macrocyclic inhibitor. The Axl crystal structure revealed two distinct conformational states of the enzyme, providing a first glimpse of what an active TAM receptor kinase may look like and suggesting a potential role for the juxtamembrane region in enzyme activity. We noted that the ATP/inhibitor-binding sites of the TAM members closely resemble each other, posing a challenge for the design of a selective inhibitor. We propose that the differences in the conformational dynamics among the TAM family members could potentially be exploited to achieve inhibitor selectivity for targeted receptors.


    Organizational Affiliation

    From Oncology Medicinal Chemistry and ketan.gajiwala@pfizer.com.,Oncology Research and Development, Pfizer Worldwide Research and Development, San Diego, California 92121.,From Oncology Medicinal Chemistry and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase receptor UFO
A, B, C, D
307Homo sapiensMutation(s): 0 
Gene Names: AXL (UFO)
EC: 2.7.10.1
Find proteins for P30530 (Homo sapiens)
Go to Gene View: AXL
Go to UniProtKB:  P30530
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7YS
Query on 7YS

Download SDF File 
Download CCD File 
A, B, C, D
(10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one
C21 H22 Cl F N6 O3
VFRJEYJOQSRCNK-LLVKDONJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.680α = 90.00
b = 100.704β = 93.97
c = 81.921γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references
  • Version 1.2: 2017-10-04
    Type: Database references