Fluorine in PDB 7khg: Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397

All present enzymatic activity of Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397:
2.7.10.1;

The structure of Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397, PDB code: 7khg was solved by Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.82 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.133, 81.961, 50.061, 90, 107.6, 90
R / Rfree (%)	18.2 / 20.3

The structure of Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397 (pdb code 7khg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397, PDB code: 7khg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:31.9 occ:1.00 F41 A:P311001 0.0 31.9 1.0 C40 A:P311001 1.4 29.4 1.0 F42 A:P311001 2.2 29.6 1.0 F43 A:P311001 2.2 31.3 1.0 C35 A:P311001 2.4 26.8 1.0 C36 A:P311001 2.8 24.1 1.0 CB A:ILE653 3.3 29.5 1.0 CG2 A:ILE653 3.4 26.9 1.0 N34 A:P311001 3.5 26.4 1.0 CD1 A:ILE653 3.5 27.6 1.0 CZ3 A:TRP557 3.8 30.9 1.0 CD2 A:LEU783 3.9 29.0 1.0 CG1 A:ILE653 4.0 26.5 1.0 C38 A:P311001 4.2 27.0 1.0 O A:ILE808 4.2 24.2 1.0 CD1 A:LEU783 4.3 24.9 1.0 CD1 A:LEU647 4.3 29.9 1.0 CA A:ILE653 4.5 28.3 1.0 CG A:LEU783 4.6 27.5 1.0 C32 A:P311001 4.6 25.6 1.0 CE3 A:TRP557 4.6 27.2 1.0 O A:VAL654 4.6 29.0 1.0 CH2 A:TRP557 4.7 25.8 1.0 C A:ILE808 4.9 25.0 1.0 N A:VAL654 4.9 26.0 1.0 C29 A:P311001 5.0 25.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:29.6 occ:1.00 F42 A:P311001 0.0 29.6 1.0 C40 A:P311001 1.4 29.4 1.0 F43 A:P311001 2.2 31.3 1.0 F41 A:P311001 2.2 31.9 1.0 C35 A:P311001 2.4 26.8 1.0 N34 A:P311001 2.7 26.4 1.0 CD1 A:LEU783 3.2 24.9 1.0 CZ3 A:TRP557 3.2 30.9 1.0 CE3 A:TRP557 3.4 27.2 1.0 CD2 A:HIS790 3.6 21.9 1.0 C36 A:P311001 3.6 24.1 1.0 CD2 A:LEU783 3.8 29.0 1.0 C32 A:P311001 4.0 25.6 1.0 CG A:LEU783 4.0 27.5 1.0 NE2 A:HIS790 4.3 22.2 1.0 CH2 A:TRP557 4.5 25.8 1.0 CG2 A:ILE808 4.6 25.0 1.0 CG A:HIS790 4.7 23.7 1.0 C38 A:P311001 4.7 27.0 1.0 CD2 A:TRP557 4.7 25.9 1.0 CD1 A:LEU647 4.8 29.9 1.0 CG2 A:ILE653 4.9 26.9 1.0 C29 A:P311001 4.9 25.2 1.0 O A:ILE808 4.9 24.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Kit Kinase Domain with A Small Molecule Inhibitor, PLX3397 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:31.3 occ:1.00 F43 A:P311001 0.0 31.3 1.0 C40 A:P311001 1.4 29.4 1.0 F42 A:P311001 2.2 29.6 1.0 F41 A:P311001 2.2 31.9 1.0 C35 A:P311001 2.4 26.8 1.0 O A:ILE808 2.8 24.2 1.0 C A:ILE808 3.0 25.0 1.0 N34 A:P311001 3.2 26.4 1.0 C36 A:P311001 3.2 24.1 1.0 CG2 A:ILE808 3.3 25.0 1.0 CB A:ILE808 3.3 24.7 1.0 N A:CYS809 3.5 24.1 1.0 CA A:ILE808 3.7 24.3 1.0 CB A:ILE653 3.8 29.5 1.0 CG2 A:ILE653 3.8 26.9 1.0 CA A:CYS809 3.8 25.6 1.0 CD1 A:LEU783 4.1 24.9 1.0 CD2 A:HIS790 4.2 21.9 1.0 C32 A:P311001 4.4 25.6 1.0 CA A:ILE653 4.4 28.3 1.0 NE2 A:HIS790 4.4 22.2 1.0 C38 A:P311001 4.5 27.0 1.0 C A:CYS809 4.5 26.3 1.0 N A:ILE808 4.6 24.2 1.0 CG1 A:ILE808 4.6 23.3 1.0 O A:CYS809 4.6 24.2 1.0 N A:VAL654 4.8 26.0 1.0 CD2 A:LEU783 4.9 29.0 1.0 CG A:LEU783 4.9 27.5 1.0 C29 A:P311001 5.0 25.2 1.0 CZ3 A:TRP557 5.0 30.9 1.0 CD1 A:ILE808 5.0 26.1 1.0

A.J.Wagner, P.L.Severson, A.F.Shields, A.Patnaik, R.Chugh, G.Tinoco, G.Wu, M.Nespi, J.Lin, Y.Zhang, T.Ewing, G.Habets, E.A.Burton, B.Matusow, J.Tsai, G.Tsang, R.Shellooe, H.Carias, K.Chan, H.Rezaei, L.Sanftner, A.Marimuthu, W.Spevak, P.N.Ibrahim, K.Inokuchi, O.Alcantar, G.Michelson, A.C.Tsiatis, C.Zhang, G.Bollag, J.C.Trent, W.D.Tap. Association of Combination of Conformation-Specific Kit Inhibitors with Clinical Benefit in Patients with Refractory Gastrointestinal Stromal Tumors Jama Oncol 2021.