6IG8

Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


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Literature

Discovery of a novel azetidine scaffold for colony stimulating factor-1 receptor (CSF-1R) Type II inhibitors by the use of docking models.

Ikegashira, K.Ikenogami, T.Yamasaki, T.Hase, Y.Yamaguchi, T.Inagaki, K.Doi, S.Adachi, T.Koga, Y.Hashimoto, H.

(2019) Bioorg Med Chem Lett 29: 115-118

  • DOI: 10.1016/j.bmcl.2018.10.051
  • Primary Citation of Related Structures:  
    6IG8

  • PubMed Abstract: 
  • We report the discovery of a novel azetidine scaffold for colony stimulating factor-1 receptor (CSF-1R) Type II inhibitors by using a structure-based drug design (SBDD) based on a docking model. The work leads to the representative compound 4a with high CSF-1R inhibitory activity (IC 50  = 9 ...

    We report the discovery of a novel azetidine scaffold for colony stimulating factor-1 receptor (CSF-1R) Type II inhibitors by using a structure-based drug design (SBDD) based on a docking model. The work leads to the representative compound 4a with high CSF-1R inhibitory activity (IC 50  = 9.1 nM). The obtained crystal structure of an azetidine compound with CSF-1R, which matched our predicted docking model, demonstrates that the azetidine compounds bind to the DFG-out conformation of the protein as a Type II inhibitor.


    Organizational Affiliation

    Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage colony-stimulating factor 1 receptor A324Homo sapiensMutation(s): 1 
Gene Names: CSF1RFMS
EC: 2.7.10.1
Find proteins for P07333 (Homo sapiens)
Explore P07333 
Go to UniProtKB:  P07333
NIH Common Fund Data Resources
PHAROS:  P07333
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A7O
Query on A7O

Download Ideal Coordinates CCD File 
A
(3-{4-[(4-cyclopropylphenyl)methoxy]-3-methoxyphenyl}azetidin-1-yl)(4-{[(2S)-2,3-dihydroxypropoxy]methyl}pyridin-2-yl)methanone
C30 H34 N2 O6
LTTJGQBDGMNWHJ-SANMLTNESA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.52α = 90
b = 62.52β = 90
c = 185.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-09-25 
  • Released Date: 2019-08-07 
  • Deposition Author(s): Doi, S., Adachi, T.

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release