8W1L: CSF1R kinase domain

Structure of CSF1R kinase domain in complex with Cpd 32. Determined by X-ray diffraction at 2.26 Å resolution. Released 29 May 2024.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,262
Mol. weight: 38.64 kDa
Ligands: A1AE3
Released: 29 May 2024

Explore 8W1L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W1L contains 18 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: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
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	625-640	16
β-strand	646	1	2
β-strand	649-653	5	1
β-strand	660-664	5	1
β-strand	670	1	2
α-helix	671-677	7
α-helix	752-771	20
α-helix	781-783	3
β-strand	784-787	4	2
α-helix	788-790	3
β-strand	791-794	4	2
α-helix	798-800	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	863-871	9
α-helix	875-878	4
α-helix	883-892	10
α-helix	897-899	3
α-helix	901-902	2
α-helix	903-912	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor,CSF1R	A	protein	333	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8W1L_1 Macrophage colony-stimulating factor 1 receptor,CSF1R (chains A)
GYKYKQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKV
VEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHG
GPVLVITEYCCYGDLLNFLRRKRPPGLEYSYNPSHNPEEQLSSRDLLHFSSQVAQGMAFL
ASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFD
CVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIM
QACWALEPTHRPTFQQICSFLQEQAQEDRRERD

Ligands and cofactors

ID	Name	Formula	Copies
A1AE3	[3-({3-methoxy-4-[(6-methoxypyridin-3-yl)methoxy]phenyl}methyl)-3H-imidazo[4,5-…	C27 H27 N5 O5	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Identification of Selective Imidazopyridine CSF1R Inhibitors. Kane Jr., J.L., Asmussen, G., Batchelor, J. et al. ACS Med Chem Lett (2024) 15:722-730. DOI 10.1021/acsmedchemlett.4c00110 · 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…
6N33 2.25 Å, Crystal structure of fms kinase domain with a small molecular inhibitor, PLX5622
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 8W1L 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.