4R7I: Macrophage colony-stimulating factor 1 receptor

Crystal structure of FMS kinase domain with a small molecular inhibitor, GLEEVEC. Determined by X-ray diffraction at 2.75 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,361
Mol. weight: 39.13 kDa
Ligands: STI
Released: 12 Aug 2015

Explore 4R7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R7I contains 21 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: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	569-572	4
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	670	1	2
α-helix	671-683	13
α-helix	748-750	3
α-helix	752-770	19
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
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	834-848	15
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	343	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4R7I_1 Macrophage colony-stimulating factor 1 receptor (chains A)
MKKGHHHHHHGQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGA
GAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLL
GACTHGGPVLVITEYCTYGDLLNFLRRKAEAMLGPSLSPGQDPEGLDKEDGRPLELRDLL
HFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNAR
LPVKWMAPESIFDSVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMA
QPAFAPKNIYSIMQACWALEPTHRPTFQQITSFLQEQAQEDRR

Ligands and cofactors

ID	Name	Formula	Copies
STI	4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-yla…	C29 H31 N7 O	1

Primary citation

Structure-Guided Blockade of CSF1R Kinase in Tenosynovial Giant-Cell Tumor. Tap, W.D., Wainberg, Z.A., Anthony, S.P. et al. N Engl J Med (2015) 373:428-437. DOI 10.1056/NEJMoa1411366 · 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
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…

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