6N33: Macrophage colony-stimulating factor 1 receptor

Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622. Determined by X-ray diffraction at 2.25 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,447
Mol. weight: 39.04 kDa
Ligands: 622
Released: 18 Sept 2019

Explore 6N33 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N33 contains 20 α-helices and 12 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: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	570-572	3
α-helix	573-575	3
β-strand	576	1	1
α-helix	579-581	3
β-strand	582-590	9	1
β-strand	594-604	11	1
β-strand	609-618	10	1
α-helix	624-640	17
β-strand	646	1	2
β-strand	649-653	5	1
β-strand	660-664	5	1
β-strand	669-670	2	2
α-helix	671-683	13
α-helix	752-771	20
α-helix	781-783	3
β-strand	784-786	3	2
α-helix	788-790	3
β-strand	792-794	3	2
α-helix	798-800	3
α-helix	803-805	3
β-strand	810-812	3	3
β-strand	815-817	3	3
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	343	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6N33_1 Macrophage colony-stimulating factor 1 receptor (chains A)
MKKGHHHHHHGQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGA
GAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLL
GACTHGGPVLVITEYCTYGDLLNFLRRKAEAMLGPSLSPGQDPEGLDKEDGRPLELRDLL
HFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNAR
LPVKWMAPESIFDSVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMA
QPAFAPKNIYSIMQACWALEPTHRPTFQQITSFLQEQAQEDRR

Ligands and cofactors

ID	Name	Formula	Copies
622	6-fluoro-N-[(5-fluoro-2-methoxypyridin-3-yl)methyl]-5-[(5-methyl-1H-pyrrolo[2,3…	C21 H19 F2 N5 O	1

Primary citation

Sustained microglial depletion with CSF1R inhibitor impairs parenchymal plaque development in an Alzheimer's disease model. Spangenberg, E., Severson, P.L., Hohsfield, L.A. et al. Nat Commun (2019) 10:3758-3758. DOI 10.1038/s41467-019-11674-z · 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
6IG8 1.8 Å, Crystal structure of CSF-1R kinase domain with a small molecular inhibitor, JTE-952
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…
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

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