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Fluorine in PDB 8s17: C-Kit Kinase Domain in Complex with Ponatinib

Enzymatic activity of C-Kit Kinase Domain in Complex with Ponatinib

All present enzymatic activity of C-Kit Kinase Domain in Complex with Ponatinib:
2.7.10.1;

Protein crystallography data

The structure of C-Kit Kinase Domain in Complex with Ponatinib, PDB code: 8s17 was solved by A.Teuber, M.P.Mueller, D.Rauh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.31 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.01, 90.61, 91.41, 90, 90, 90
R / Rfree (%) 20.1 / 22.8

Other elements in 8s17:

The structure of C-Kit Kinase Domain in Complex with Ponatinib also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the C-Kit Kinase Domain in Complex with Ponatinib (pdb code 8s17). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the C-Kit Kinase Domain in Complex with Ponatinib, PDB code: 8s17:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8s17

Go back to Fluorine Binding Sites List in 8s17
Fluorine binding site 1 out of 6 in the C-Kit Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of C-Kit Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:41.7
occ:1.00
 F1 A:0LI1001 0.0 41.7 1.0
C19 A:0LI1001 1.3 45.2 1.0
F3 A:0LI1001 2.1 43.4 1.0
F2 A:0LI1001 2.1 41.1 1.0
C17 A:0LI1001 2.4 40.0 1.0
C16 A:0LI1001 3.0 45.3 1.0
C20 A:0LI1001 3.1 42.6 1.0
C18 A:0LI1001 3.4 39.5 1.0
CD1 A:LEU647 3.6 37.8 1.0
CG2 A:ILE653 3.7 41.1 1.0
CD2 A:LEU783 3.9 40.7 1.0
CD1 A:LEU783 4.0 41.6 1.0
C15 A:0LI1001 4.3 42.7 1.0
N3 A:0LI1001 4.5 45.8 1.0
CD2 A:LEU644 4.5 42.9 1.0
CG A:LEU783 4.6 43.5 1.0
C13 A:0LI1001 4.7 47.3 1.0
CD1 A:ILE653 4.9 43.6 1.0
C14 A:0LI1001 5.0 46.8 1.0

Fluorine binding site 2 out of 6 in 8s17

Go back to Fluorine Binding Sites List in 8s17
Fluorine binding site 2 out of 6 in the C-Kit Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of C-Kit Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:41.1
occ:1.00
 F2 A:0LI1001 0.0 41.1 1.0
C19 A:0LI1001 1.3 45.2 1.0
F1 A:0LI1001 2.1 41.7 1.0
F3 A:0LI1001 2.1 43.4 1.0
C17 A:0LI1001 2.4 40.0 1.0
C16 A:0LI1001 3.0 45.3 1.0
C20 A:0LI1001 3.2 42.6 1.0
CD2 A:HIS790 3.2 38.8 1.0
C18 A:0LI1001 3.4 39.5 1.0
NE2 A:HIS790 3.5 37.5 1.0
CG2 A:ILE808 3.7 39.2 1.0
O A:CYS809 3.8 37.3 1.0
C A:CYS809 3.9 35.6 1.0
CD1 A:LEU783 4.1 41.6 1.0
CA A:CYS809 4.2 35.4 1.0
N A:CYS809 4.3 39.2 1.0
N A:ASP810 4.3 38.2 1.0
C15 A:0LI1001 4.3 42.7 1.0
CG A:HIS790 4.3 39.7 1.0
N3 A:0LI1001 4.4 45.8 1.0
CB A:ASP810 4.4 41.7 1.0
C21 A:0LI1001 4.4 42.4 1.0
C A:ILE808 4.5 36.6 1.0
O A:ILE808 4.6 39.6 1.0
CE1 A:HIS790 4.6 42.9 1.0
C13 A:0LI1001 4.6 47.3 1.0
CB A:ILE808 4.7 39.5 1.0
CA A:ASP810 4.9 40.7 1.0
CG2 A:ILE653 5.0 41.1 1.0
C14 A:0LI1001 5.0 46.8 1.0

Fluorine binding site 3 out of 6 in 8s17

Go back to Fluorine Binding Sites List in 8s17
Fluorine binding site 3 out of 6 in the C-Kit Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of C-Kit Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:43.4
occ:1.00
 F3 A:0LI1001 0.0 43.4 1.0
C19 A:0LI1001 1.3 45.2 1.0
F1 A:0LI1001 2.1 41.7 1.0
F2 A:0LI1001 2.1 41.1 1.0
C17 A:0LI1001 2.4 40.0 1.0
C18 A:0LI1001 2.7 39.5 1.0
O A:ILE808 3.1 39.6 1.0
CG2 A:ILE653 3.4 41.1 1.0
CA A:CYS809 3.4 35.4 1.0
C A:ILE808 3.6 36.6 1.0
C16 A:0LI1001 3.7 45.3 1.0
N A:CYS809 3.8 39.2 1.0
C A:CYS809 3.9 35.6 1.0
C13 A:0LI1001 4.1 47.3 1.0
CG1 A:VAL654 4.1 37.4 1.0
CG2 A:ILE808 4.2 39.2 1.0
N A:ASP810 4.3 38.2 1.0
O A:CYS809 4.4 37.3 1.0
C20 A:0LI1001 4.4 42.6 1.0
O1 A:0LI1001 4.4 44.9 1.0
CB A:ILE808 4.6 39.5 1.0
CB A:CYS809 4.7 36.0 1.0
CA A:ILE808 4.7 37.4 1.0
CD2 A:LEU644 4.7 42.9 1.0
N A:VAL654 4.7 41.3 1.0
C15 A:0LI1001 4.7 42.7 1.0
CB A:ILE653 4.8 45.6 1.0
N2 A:0LI1001 4.8 42.9 1.0
C14 A:0LI1001 4.9 46.8 1.0
C12 A:0LI1001 4.9 42.3 1.0

Fluorine binding site 4 out of 6 in 8s17

Go back to Fluorine Binding Sites List in 8s17
Fluorine binding site 4 out of 6 in the C-Kit Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of C-Kit Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:54.6
occ:1.00
 F1 B:0LI1001 0.0 54.6 1.0
C19 B:0LI1001 1.3 51.5 1.0
F2 B:0LI1001 2.1 55.4 1.0
F3 B:0LI1001 2.1 48.5 1.0
C17 B:0LI1001 2.4 53.7 1.0
C18 B:0LI1001 2.6 54.1 1.0
O B:ILE808 3.1 46.8 1.0
CA B:CYS809 3.4 51.9 1.0
CG2 B:ILE653 3.5 54.1 1.0
C B:ILE808 3.6 54.7 1.0
C16 B:0LI1001 3.7 50.9 1.0
N B:CYS809 3.8 52.2 1.0
CG1 B:VAL654 3.8 49.4 1.0
C B:CYS809 3.9 48.8 1.0
C13 B:0LI1001 4.0 56.1 1.0
CG2 B:ILE808 4.2 50.6 1.0
N B:ASP810 4.2 50.3 1.0
O1 B:0LI1001 4.2 52.9 1.0
C20 B:0LI1001 4.4 46.8 1.0
O B:CYS809 4.5 52.2 1.0
CB B:ILE808 4.6 53.7 1.0
CB B:CYS809 4.7 45.0 1.0
N B:VAL654 4.7 50.6 1.0
C15 B:0LI1001 4.7 57.0 1.0
CA B:ILE808 4.7 49.9 1.0
N2 B:0LI1001 4.7 57.2 1.0
CB B:ILE653 4.8 59.8 1.0
CD2 B:LEU644 4.8 64.4 1.0
C12 B:0LI1001 4.8 54.4 1.0
C14 B:0LI1001 4.9 55.6 1.0
CB B:VAL654 5.0 48.6 1.0

Fluorine binding site 5 out of 6 in 8s17

Go back to Fluorine Binding Sites List in 8s17
Fluorine binding site 5 out of 6 in the C-Kit Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of C-Kit Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:55.4
occ:1.00
 F2 B:0LI1001 0.0 55.4 1.0
C19 B:0LI1001 1.3 51.5 1.0
F1 B:0LI1001 2.1 54.6 1.0
F3 B:0LI1001 2.2 48.5 1.0
C17 B:0LI1001 2.4 53.7 1.0
C16 B:0LI1001 3.0 50.9 1.0
C20 B:0LI1001 3.1 46.8 1.0
CD1 B:LEU647 3.4 59.9 1.0
C18 B:0LI1001 3.4 54.1 1.0
CG2 B:ILE653 3.7 54.1 1.0
CD2 B:LEU783 4.0 63.2 1.0
CD1 B:LEU783 4.1 59.7 1.0
CD1 B:ILE653 4.3 67.9 1.0
C15 B:0LI1001 4.3 57.0 1.0
N3 B:0LI1001 4.5 53.0 1.0
CG B:LEU783 4.6 54.9 1.0
C13 B:0LI1001 4.6 56.1 1.0
CD2 B:LEU644 4.7 64.4 1.0
CG B:LEU647 4.9 63.3 1.0
O B:ILE808 5.0 46.8 1.0
C14 B:0LI1001 5.0 55.6 1.0

Fluorine binding site 6 out of 6 in 8s17

Go back to Fluorine Binding Sites List in 8s17
Fluorine binding site 6 out of 6 in the C-Kit Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of C-Kit Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:48.5
occ:1.00
 F3 B:0LI1001 0.0 48.5 1.0
C19 B:0LI1001 1.3 51.5 1.0
F1 B:0LI1001 2.1 54.6 1.0
F2 B:0LI1001 2.2 55.4 1.0
C17 B:0LI1001 2.4 53.7 1.0
C16 B:0LI1001 3.0 50.9 1.0
C20 B:0LI1001 3.2 46.8 1.0
C18 B:0LI1001 3.4 54.1 1.0
CD2 B:HIS790 3.4 46.7 1.0
NE2 B:HIS790 3.6 46.6 1.0
CG2 B:ILE808 3.8 50.6 1.0
C B:CYS809 4.0 48.8 1.0
O B:CYS809 4.1 52.2 1.0
C21 B:0LI1001 4.2 53.4 1.0
CD1 B:LEU783 4.2 59.7 1.0
N3 B:0LI1001 4.2 53.0 1.0
CA B:CYS809 4.2 51.9 1.0
N B:ASP810 4.3 50.3 1.0
CB B:ASP810 4.3 50.7 1.0
C15 B:0LI1001 4.3 57.0 1.0
CG B:HIS790 4.4 46.9 1.0
N B:CYS809 4.4 52.2 1.0
C B:ILE808 4.6 54.7 1.0
CE1 B:HIS790 4.6 45.4 1.0
C13 B:0LI1001 4.6 56.1 1.0
O B:ILE808 4.6 46.8 1.0
CB B:ILE808 4.8 53.7 1.0
CA B:ASP810 4.9 51.8 1.0
C14 B:0LI1001 5.0 55.6 1.0

Reference:

A.Teuber, J.Niggenaber, S.B.Kleinboelting, I.Landel, J.Warmuth, D.Busick, M.P.Mueller, S.Bauer, D.Rauh. C-Kit Kinase Domain in Complex with Ponatinib To Be Published.
Page generated: Sat Dec 13 15:39:27 2025

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