ISDA

Deposition Date 2018-09-25

Release Date 2019-08-07

Last Version Date 2023-11-22

Entry Detail

PDB ID:

6IG8

Keywords:

TRANSFERASE/TRANSFERASE INHIBITOR

Title:

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

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.80 Å

R-Value Free:

0.19

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

P 43 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Macrophage colony-stimulating factor 1 receptor
Gene (Uniprot):CSF1R
Mutations:S688A
Chain IDs:A
Chain Length:324
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P07333 Pfam ID:PF07714 EC:2.7.10.1

Ligand Molecules

A7O

GOL

Primary Citation

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.Show

Bioorg.Med.Chem.Lett. 29 115 118 (2019)

PMID: 30442420 DOI: 10.1016/j.bmcl.2018.10.051

Abstact

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 (IC50 = 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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Primary Citation of related structures