7TNH: CSF1R kinase domain

Crystal structure of CSF1R kinase domain in complex with DP-6233. Determined by X-ray diffraction at 2.7 Å resolution. Released 24 Aug 2022.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,122
Mol. weight: 39.08 kDa
Ligands: I9W
Released: 24 Aug 2022

Explore 7TNH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TNH contains 17 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	552	1	1
α-helix	570-572	3
α-helix	573-575	3
β-strand	576	1	2
α-helix	579-581	3
β-strand	582-590	9	2
β-strand	595-601	7	2
β-strand	612-617	6	2
α-helix	624-640	17
β-strand	646	1	3
β-strand	649-653	5	2
β-strand	660-663	4	2
β-strand	669-670	2	3
α-helix	671-677	7
α-helix	699-771	20
β-strand	774	1	1
α-helix	781-783	3
β-strand	784-787	4	3
β-strand	791-794	4	3
α-helix	798-800	3
β-strand	810-812	3	4
β-strand	815-817	3	4
α-helix	819-821	3
α-helix	824-829	6
α-helix	834-850	17
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	903-911	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor,Fibroblast growth factor receptor 1 chimera	A	protein	338	Homo sapiens	P07333 (AlphaFold model), P11362 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7TNH_1 Macrophage colony-stimulating factor 1 receptor,Fibroblast growth factor receptor 1 chimera (chains A)
MHHHHHHHHENLYFQGSRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAG
AFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLG
ACTHGGPVLVITEYCCYGDLLNFLRRKRPPGLEYSYNPSHNPEEQLSSRDLLHFSSQVAQ
GMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAP
ESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKN
IYSIMQACWALEPTHRPTFQQICSFLQEQAQEDRRERD

Ligands and cofactors

ID	Name	Formula	Copies
I9W	2,2-dimethyl-N-[(6-methyl-5-{[2-(1-methyl-1H-pyrazol-4-yl)pyridin-4-yl]oxy}pyri…	C21 H24 N6 O3	1

Water and common crystallization additives (NA, CL) are not listed.

Primary citation

Discovery of acyl ureas as highly selective small molecule CSF1R kinase inhibitors. Caldwell, T.M., Kaufman, M.D., Wise, S.C. et al. Bioorg Med Chem Lett (2022) 74:128929-128929. DOI 10.1016/j.bmcl.2022.128929 · 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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