2I0V | pdb_00002i0v

c-FMS tyrosine kinase in complex with a quinolone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.296 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.266 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2I0V

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Crystal structure of the tyrosine kinase domain of colony-stimulating factor-1 receptor (cFMS) in complex with two inhibitors.

Schubert, C.Schalk-Hihi, C.Struble, G.T.Ma, H.C.Petrounia, I.P.Brandt, B.Deckman, I.C.Patch, R.J.Player, M.R.Spurlino, J.C.Springer, B.A.

(2007) J Biological Chem 282: 4094-4101

  • DOI: https://doi.org/10.1074/jbc.M608183200
  • Primary Citation Related Structures: 
    2I0V, 2I0Y, 2I1M

  • PubMed Abstract: 

    The cFMS proto-oncogene encodes for the colony-stimulating factor-1 receptor, a receptor-tyrosine kinase responsible for the differentiation and maturation of certain macrophages. Upon binding its ligand colony-stimulating factor-1 cFMS autophosphorylates, dimerizes, and induces phosphorylation of downstream targets. We report the novel crystal structure of unphosphorylated cFMS in complex with two members of different classes of drug-like protein kinase inhibitors. cFMS exhibits a typical bi-lobal kinase fold, and its activation loop and DFG motif are found to be in the canonical inactive conformation. Both ATP competitive inhibitors are bound in the active site and demonstrate a binding mode similar to that of STI-571 bound to cABL. The DFG motif is prevented from switching into the catalytically competent conformation through interactions with the inhibitors. Activation of cFMS is also inhibited by the juxtamembrane domain, which interacts with residues of the active site and prevents formation of the activated kinase. Together the structures of cFMS provide further insight into the autoinhibition of receptor-tyrosine kinases via their respective juxtamembrane domains; additionally the binding mode of two novel classes of kinase inhibitors will guide the design of novel molecules targeting macrophage-related diseases.


  • Organizational Affiliation
    • Structural Biology, Johnson & Johnson Pharmaceuticals Research and Development, LLC, Exton, Pennsylvania 19341, USA. cschuber@prdus.jnj.com

Macromolecule Content 

  • Total Structure Weight: 38.5 kDa 
  • Atom Count: 2,456 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 335 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cFMS tyrosine kinase335Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P07333 (Homo sapiens)
Explore P07333 
Go to UniProtKB:  P07333
PHAROS:  P07333
GTEx:  ENSG00000182578 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07333
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6C3

Query on 6C3



Download:Ideal Coordinates CCD File
C [auth A]6-CHLORO-3-(3-METHYLISOXAZOL-5-YL)-4-PHENYLQUINOLIN-2(1H)-ONE
C19 H13 Cl N2 O2
QINNOQKHPLWGBK-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.296 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.266 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.199α = 90
b = 82.199β = 90
c = 143.3γ = 120
Software Package:
Software NamePurpose
CNXrefinement
PROTEUM PLUSdata collection
SAINTdata reduction
LSCALEdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references, Derived calculations