6IG8 | pdb_00006ig8

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

• PDB DOI: https://doi.org/10.2210/pdb6IG8/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

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

• PubMed: 30442420 
• DOI: https://doi.org/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  = 9.1 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.94 kDa 
• Atom Count: 2,901 
• Modelled Residue Count: 301 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage colony-stimulating factor 1 receptor	A	324	Homo sapiens	Mutation(s): 1  Gene Names: CSF1R, FMS 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A7O (Subject of Investigation/LOI)	E [auth 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
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A7O	BindingDB:  6IG8	IC50: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.52	α = 90
b = 62.52	β = 90
c = 185.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description