4UWB

Fibroblast growth factor receptor 1 kinase in complex with JK-P5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Validation of IMS-MS as a screening tool to identify type II kinase inhibitors of FGFR1 kinase.

Beeston, H.S.Klein, T.Norman, R.A.Tucker, J.A.Anderson, M.Ashcroft, A.E.Holdgate, G.A.

(2021) Rapid Commun Mass Spectrom : e9130-e9130

  • DOI: https://doi.org/10.1002/rcm.9130
  • Primary Citation of Related Structures:  
    4UWB, 4UWC

  • PubMed Abstract: 

    The protein kinase FGFR1 regulates cellular processes in human development. As over-activity of FGFR1 is implicated with cancer, effective inhibitors are in demand. Type I inhibitors, which bind to the active form of FGFR1, are less effective than type II inhibitors, which bind to the inactive form. Screening to distinguish between type I and type II inhibitors is required. X-ray crystallography was used to indicate whether a range of potential inhibitors bind to the active or inactive FGFR1 kinase conformation. The binding affinity of each ligand to FGFR1 was measured using biochemical methods. Electrospray ionisation - ion mobility spectrometry - mass spectrometry (ESI-IMS-MS) in conjunction with collision-induced protein unfolding generated a conformational profile of each FGFR1-ligand complex. The results indicate that the protein's conformational profile depends on whether the inhibitor is type I or type II. X-ray crystallography confirmed which of the kinase inhibitors bind to the active or inactive form of FGFR1 kinase. Collision-induced unfolding combined with ESI-IMS-MS showed distinct differences in the FGFR1 folding landscape for type I and type II inhibitors. Biochemical studies indicated a similar range of FGFR1 affinities for both types of inhibitors, thus providing confidence that the conformational variations detected using ESI-IMS-MS can be interpretated unequivocally and that this is an effective screening method. A robust ESI-IMS-MS method has been implemented to distinguish between the binding mode of type I and type II inhibitors by monitoring the conformational unfolding profile of FGFR1. This rapid method requires low sample concentrations and could be used as a high-throughput screening technique for the characterisation of novel kinase inhibitors.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology & Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FIBROBLAST GROWTH FACTOR RECEPTOR 1
A, B
309Homo sapiensMutation(s): 2 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens)
Explore P11362 
Go to UniProtKB:  P11362
PHAROS:  P11362
GTEx:  ENSG00000077782 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11362
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JVT
Query on JVT

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
N-[4-(4-methylpiperazin-1-yl)phenyl]-1H-indazole-3-carboxamide
C19 H21 N5 O
NZDNAXLFPOOOJE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.623α = 90
b = 57.323β = 107.58
c = 65.628γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Other
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2021-06-16
    Changes: Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Refinement description