8JOT: CSF-1R kinase domain with sulfatinib

Crystal structure of CSF-1R kinase domain with sulfatinib. Determined by X-ray diffraction at 1.69 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,722
Mol. weight: 40.51 kDa
Ligands: UKI
Released: 27 Mar 2024

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

Secondary structure: helices and β-sheets

8JOT 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	570-571	2
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	670	1	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	784-786	3	4
α-helix	788-790	3
β-strand	792-794	3	4
α-helix	798-800	3
α-helix	803-805	3
β-strand	810-811	2	5
β-strand	816-817	2	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	903-913	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor	A	protein	354	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8JOT_1 Macrophage colony-stimulating factor 1 receptor (chains A)
MKKGHHHHHHGQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGA
GAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLL
GACTHGGPVLVITEYCTYGDLLNFLRRKAEAMLGPSLSPGQDPEGGVDYKNIHLEKLDKE
DGRPLELRDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMN
DSNYIVKGNARLPVKWMAPESIFDSVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKF
YKLVKDGYQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQITSFLQEQAQEDRR

Ligands and cofactors

ID	Name	Formula	Copies
UKI	Sulfatinib	C24 H28 N6 O3 S	1

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

Primary citation

Structural basis and selectivity of sulfatinib binding to FGFR and CSF-1R. Lin, Q., Dai, S., Qu, L. et al. Commun Chem (2024) 7:3-3. DOI 10.1038/s42004-023-01084-0 · PubMed

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

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
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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