6IG8: Macrophage colony-stimulating factor 1 receptor

Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952. Determined by X-ray diffraction at 1.8 Å resolution. Released 7 Aug 2019.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,901
Mol. weight: 36.94 kDa
Ligands: A7O, MG
Released: 7 Aug 2019

Explore 6IG8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IG8 contains 22 α-helices and 16 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	551-552	2	1
β-strand	553	1	2
β-strand	563	1	2
α-helix	566-568	3
α-helix	570-572	3
α-helix	573-575	3
β-strand	576	1	3
α-helix	579-581	3
β-strand	582-590	9	3
β-strand	594-604	11	3
β-strand	609-618	10	3
α-helix	624-640	17
β-strand	646	1	4
β-strand	649-653	5	3
β-strand	660-664	5	3
β-strand	669-670	2	4
α-helix	671-683	13
α-helix	748-750	3
α-helix	752-771	20
β-strand	774-775	2	1
α-helix	781-783	3
β-strand	784-787	4	4
α-helix	788-790	3
β-strand	791-794	4	4
α-helix	798-800	3
α-helix	803-805	3
β-strand	810-812	3	5
β-strand	815-817	3	5
α-helix	819-821	3
α-helix	824-829	6
α-helix	834-849	16
α-helix	853-854	2
α-helix	863-870	8
α-helix	875-878	4
α-helix	883-892	10
α-helix	897-899	3
α-helix	901-902	2
α-helix	903-914	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor	A	protein	324	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6IG8_1 Macrophage colony-stimulating factor 1 receptor (chains A)
WKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDA
VLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCCYG
DLLNFLRRKAEAMLGPSLAPGQDPEGLDKEDGRPLELRDLLHFSSQVAQGMAFLASKNCI
HRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDCVYTVQ
SDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACWAL
EPTHRPTFQQICSFLQEQAQEDRR

Ligands and cofactors

ID	Name	Formula	Copies
A7O	(3-{4-[(4-cyclopropylphenyl)methoxy]-3-methoxyphenyl}azetidin-1-yl)(4-{[(2S)-2,…	C30 H34 N2 O6	1
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL) are not listed.

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. et al. Bioorg Med Chem Lett (2019) 29:115-118. DOI 10.1016/j.bmcl.2018.10.051 · PubMed

Other PDB entries of the same protein (UniProt P07333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JOT 1.69 Å, Crystal structure of CSF-1R kinase domain with sulfatinib
6T2W 1.7 Å, Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4)
2I1M 1.8 Å, cFMS tyrosine kinase (tie2 KID) in complex with an arylamide inhibitor
2I0Y 1.9 Å, cFMS tyrosine kinase (FGF KID) in complex with an arylamide inhibitor
8CGC 1.93 Å, Structure of CSF1R in complex with a pyrollopyrimidine (compound 23)
3DPK 1.95 Å, cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor
3BEA 2.02 Å, cFMS tyrosine kinase (tie2 KID) in complex with a pyrimidinopyridone inhibitor
3KRJ 2.1 Å, cFMS tyrosine kinase in complex with 4-Cyano-1H-imidazole-2-carboxylic acid…
6N33 2.25 Å, Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622
8W1L 2.26 Å, Structure of CSF1R kinase domain in complex with Cpd 32
3KRL 2.4 Å, cFMS Tyrosine kinase in complex with 5-Cyano-furan-2-carboxylic acid…
3LCD 2.5 Å, Inhibitor Bound to A DFG-In structure of the Kinase Domain of CSF-1R

Browse structure collections

About this viewer

MolViewer shows 6IG8 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.