3DPK: CFMS tyrosine kinase

cFMS tyrosine kinase in complex with a pyridopyrimidinone inhibitor. Determined by X-ray diffraction at 1.95 Å resolution. Released 17 Feb 2009.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,387
Mol. weight: 38.84 kDa
Ligands: 8C5
Released: 17 Feb 2009

Explore 3DPK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DPK contains 18 α-helices and 14 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	551-552	2	1
α-helix	573-575	3
β-strand	576	1	2
α-helix	579-581	3
β-strand	582-590	9	2
β-strand	594-602	9	2
β-strand	610-618	9	2
α-helix	624-640	17
β-strand	646	1	3
β-strand	649-653	5	2
β-strand	660-664	5	2
β-strand	669-670	2	3
α-helix	671-676	6
α-helix	699-771	20
β-strand	774-775	2	1
α-helix	781-783	3
β-strand	784-787	4	3
α-helix	788-790	3
β-strand	791-794	4	3
α-helix	803-805	3
β-strand	810	1	4
β-strand	817	1	4
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	903-911	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor, Fibroblast growth factor receptor 1	A	protein	335	Homo sapiens	P07333 (AlphaFold model), P11362 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DPK_1 Macrophage colony-stimulating factor 1 receptor, Fibroblast growth factor receptor 1 (chains A)
GVDYKYKQKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFG
KVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACT
HGGPVLVITEYCCYGDLLNFLRRKRPPGLEYSYNPSHNPEEQLSSRDLLHFSSQVAQGMA
FLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESI
FDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYS
IMQACWALEPTHRPTFQQICSFLQEQAQEDRRERD

Ligands and cofactors

ID	Name	Formula	Copies
8C5	8-cyclohexyl-N-methoxy-5-oxo-2-{[4-(2-pyrrolidin-1-ylethyl)phenyl]amino}-5,8-di…	C27 H34 N6 O3	1

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

Primary citation

Pyrido[2,3-d]pyrimidin-5-ones: a novel class of antiinflammatory macrophage colony-stimulating factor-1 receptor inhibitors. Huang, H., Hutta, D.A., Rinker, J.M. et al. J Med Chem (2009) 52:1081-1099. DOI 10.1021/jm801406h · 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)
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

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