6T2W: Macrophage colony-stimulating factor 1 receptor

Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4). Determined by X-ray diffraction at 1.7 Å resolution. Released 1 Jan 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,669
Mol. weight: 38.1 kDa
Ligands: M9T
Released: 1 Jan 2020

Explore 6T2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T2W 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	566-568	3
α-helix	573-575	3
β-strand	576	1	2
α-helix	579-581	3
β-strand	582-590	9	2
β-strand	594-604	11	2
β-strand	609-618	10	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	670	1	3
α-helix	671-680	10
α-helix	752-771	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
β-strand	810-812	3	4
β-strand	815-817	3	4
α-helix	819-821	3
α-helix	824-829	6
α-helix	834-849	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	903-915	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Macrophage colony-stimulating factor 1 receptor	A	protein	332	Homo sapiens	P07333 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6T2W_1 Macrophage colony-stimulating factor 1 receptor (chains A)
QKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATA
FGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLV
ITEYCCYGDLLNFLRRKAEAMLGPSLSPGQDPEGLDKEDGRPLELRDLLHFSSQVAQGMA
FLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESI
FDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYS
IMQACWALEPTHRPTFQQICSFLQEQAQEDRR

Ligands and cofactors

ID	Name	Formula	Copies
M9T	2-[(4-methoxy-2-methyl-phenyl)amino]-7-methyl-9-(4-oxidanylcyclohexyl)purin-8-o…	C20 H25 N5 O3	1

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

Primary citation

The Discovery of 7-Methyl-2-[(7-methyl[1,2,4]triazolo[1,5-a]pyridin-6-yl)amino]-9-(tetrahydro-2H-pyran-4-yl)-7,9-dihydro-8H-purin-8-one (AZD7648), a Potent and Selective DNA-Dependent Protein Kinase (DNA-PK) Inhibitor. Goldberg, F.W., Finlay, M.R.V., Ting, A.K.T. et al. J Med Chem (2020) 63:3461-3471. DOI 10.1021/acs.jmedchem.9b01684 · 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
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

Browse structure collections

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