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Fluorine in PDB 7ote: Src Kinase Domain in Complex with Ponatinib

Enzymatic activity of Src Kinase Domain in Complex with Ponatinib

All present enzymatic activity of Src Kinase Domain in Complex with Ponatinib:
2.7.10.2;

Protein crystallography data

The structure of Src Kinase Domain in Complex with Ponatinib, PDB code: 7ote was solved by P.Soriano-Maldonado, H.N.Cuesta-Hernandez, I.Plaza-Menacho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.59 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.153, 124.631, 63.591, 90, 90.15, 90
R / Rfree (%) 17.5 / 25.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Src Kinase Domain in Complex with Ponatinib (pdb code 7ote). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Src Kinase Domain in Complex with Ponatinib, PDB code: 7ote:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ote

Go back to Fluorine Binding Sites List in 7ote
Fluorine binding site 1 out of 6 in the Src 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 Src Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:57.3
occ:1.00
 F1 A:0LI601 0.0 57.3 1.0
C19 A:0LI601 1.3 56.2 1.0
F3 A:0LI601 2.1 56.9 1.0
F2 A:0LI601 2.2 55.3 1.0
C17 A:0LI601 2.4 54.4 1.0
C18 A:0LI601 3.1 54.2 1.0
O A:VAL405 3.2 32.9 1.0
C16 A:0LI601 3.4 55.4 1.0
CG1 A:VAL405 3.6 28.1 1.0
C A:VAL405 3.6 30.5 1.0
C20 A:0LI601 3.8 55.9 1.0
C A:ALA406 3.8 41.6 1.0
O A:ALA406 3.9 39.5 1.0
CA A:ALA406 4.0 38.6 1.0
N A:ALA406 4.0 33.9 1.0
CD2 A:HIS387 4.0 38.6 1.0
CB A:VAL405 4.1 27.6 1.0
NE2 A:HIS387 4.1 37.8 1.0
CD1 A:LEU325 4.1 39.9 1.0
N A:ASP407 4.4 44.0 1.0
C13 A:0LI601 4.4 55.0 1.0
CA A:VAL405 4.5 28.1 1.0
C15 A:0LI601 4.6 55.1 1.0
CB A:ASP407 4.8 46.3 1.0
CG A:LEU325 4.9 40.6 1.0
C14 A:0LI601 5.0 53.5 1.0

Fluorine binding site 2 out of 6 in 7ote

Go back to Fluorine Binding Sites List in 7ote
Fluorine binding site 2 out of 6 in the Src 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 Src Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:55.3
occ:1.00
 F2 A:0LI601 0.0 55.3 1.0
C19 A:0LI601 1.3 56.2 1.0
F3 A:0LI601 2.1 56.9 1.0
F1 A:0LI601 2.2 57.3 1.0
C17 A:0LI601 2.3 54.4 1.0
C18 A:0LI601 2.6 54.2 1.0
O A:VAL405 3.2 32.9 1.0
CD1 A:LEU325 3.6 39.9 1.0
C16 A:0LI601 3.7 55.4 1.0
CB A:LEU325 3.9 37.6 1.0
O A:VAL326 3.9 44.0 1.0
N A:VAL326 3.9 38.8 1.0
C13 A:0LI601 3.9 55.0 1.0
CA A:LEU325 4.1 37.6 1.0
C A:LEU325 4.2 36.0 1.0
C A:VAL405 4.2 30.5 1.0
CG A:LEU325 4.3 40.6 1.0
C20 A:0LI601 4.4 55.9 1.0
CA A:ALA406 4.5 38.6 1.0
N2 A:0LI601 4.6 57.7 1.0
C15 A:0LI601 4.7 55.1 1.0
CA A:VAL326 4.7 40.4 1.0
C A:VAL326 4.8 39.8 1.0
N A:ALA406 4.8 33.9 1.0
C14 A:0LI601 4.8 53.5 1.0
C A:ALA406 4.9 41.6 1.0
O A:LEU325 4.9 35.3 1.0
CB A:VAL326 4.9 40.7 1.0
CD2 A:LEU325 5.0 40.4 1.0

Fluorine binding site 3 out of 6 in 7ote

Go back to Fluorine Binding Sites List in 7ote
Fluorine binding site 3 out of 6 in the Src 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 Src Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:56.9
occ:1.00
 F3 A:0LI601 0.0 56.9 1.0
C19 A:0LI601 1.3 56.2 1.0
F2 A:0LI601 2.1 55.3 1.0
F1 A:0LI601 2.1 57.3 1.0
C17 A:0LI601 2.3 54.4 1.0
C20 A:0LI601 2.9 55.9 1.0
C16 A:0LI601 3.0 55.4 1.0
CD1 A:LEU325 3.1 39.9 1.0
C18 A:0LI601 3.5 54.2 1.0
C15 A:0LI601 4.3 55.1 1.0
CG A:LEU320 4.3 48.5 1.0
N3 A:0LI601 4.3 57.7 1.0
CD2 A:LEU320 4.3 51.1 1.0
CG A:LEU325 4.4 40.6 1.0
CB A:LEU325 4.7 37.6 1.0
C13 A:0LI601 4.7 55.0 1.0
O A:VAL405 4.8 32.9 1.0
CG2 A:VAL380 4.9 36.4 1.0
C21 A:0LI601 4.9 56.5 1.0
C24 A:0LI601 4.9 57.5 1.0
CB A:LEU320 4.9 50.9 1.0

Fluorine binding site 4 out of 6 in 7ote

Go back to Fluorine Binding Sites List in 7ote
Fluorine binding site 4 out of 6 in the Src 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 Src Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:41.9
occ:1.00
 F1 B:0LI601 0.0 41.9 1.0
C19 B:0LI601 1.3 39.0 1.0
F3 B:0LI601 2.2 35.5 1.0
F2 B:0LI601 2.2 41.1 1.0
C17 B:0LI601 2.3 38.2 1.0
C18 B:0LI601 2.6 38.6 1.0
CA B:ALA406 3.3 41.6 1.0
O B:VAL405 3.4 39.3 1.0
C B:VAL405 3.6 36.4 1.0
N B:ALA406 3.6 39.3 1.0
C16 B:0LI601 3.7 37.5 1.0
C B:ALA406 3.7 42.6 1.0
CG1 B:VAL405 3.9 29.7 1.0
C13 B:0LI601 4.0 38.5 1.0
CD2 B:LEU325 4.0 48.2 1.0
O B:ALA406 4.1 36.3 1.0
N B:ASP407 4.2 48.7 1.0
CB B:VAL405 4.3 27.3 1.0
C20 B:0LI601 4.4 40.5 1.0
CB B:LEU325 4.5 40.8 1.0
CA B:VAL405 4.6 29.6 1.0
CG B:LEU325 4.6 45.3 1.0
CD1 B:LEU325 4.7 45.7 1.0
CB B:ALA406 4.7 40.7 1.0
N2 B:0LI601 4.7 41.6 1.0
C15 B:0LI601 4.7 37.9 1.0
CD2 B:HIS387 4.8 36.5 1.0
C14 B:0LI601 4.8 36.3 1.0
CB B:ASP407 4.9 51.2 1.0
N B:VAL326 4.9 42.5 1.0
NE2 B:HIS387 5.0 33.7 1.0
CA B:LEU325 5.0 40.0 1.0

Fluorine binding site 5 out of 6 in 7ote

Go back to Fluorine Binding Sites List in 7ote
Fluorine binding site 5 out of 6 in the Src 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 Src Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:41.1
occ:1.00
 F2 B:0LI601 0.0 41.1 1.0
C19 B:0LI601 1.3 39.0 1.0
F3 B:0LI601 2.1 35.5 1.0
F1 B:0LI601 2.2 41.9 1.0
C17 B:0LI601 2.4 38.2 1.0
C16 B:0LI601 3.2 37.5 1.0
C20 B:0LI601 3.4 40.5 1.0
C18 B:0LI601 3.4 38.6 1.0
CD1 B:LEU325 3.4 45.7 1.0
CD1 B:LEU320 3.7 53.8 1.0
CD2 B:LEU325 3.9 48.2 1.0
CG B:LEU325 4.1 45.3 1.0
CB B:LEU325 4.3 40.8 1.0
N3 B:0LI601 4.3 41.3 1.0
C15 B:0LI601 4.5 37.9 1.0
C13 B:0LI601 4.6 38.5 1.0
CG B:LEU320 4.9 53.2 1.0
CB B:LEU320 4.9 54.5 1.0

Fluorine binding site 6 out of 6 in 7ote

Go back to Fluorine Binding Sites List in 7ote
Fluorine binding site 6 out of 6 in the Src 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 Src Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:35.5
occ:1.00
 F3 B:0LI601 0.0 35.5 1.0
C19 B:0LI601 1.3 39.0 1.0
F2 B:0LI601 2.1 41.1 1.0
F1 B:0LI601 2.2 41.9 1.0
C17 B:0LI601 2.3 38.2 1.0
C16 B:0LI601 2.9 37.5 1.0
C20 B:0LI601 3.0 40.5 1.0
N3 B:0LI601 3.3 41.3 1.0
C18 B:0LI601 3.5 38.6 1.0
CD2 B:HIS387 3.7 36.5 1.0
C24 B:0LI601 4.0 40.7 1.0
NE2 B:HIS387 4.2 33.7 1.0
C15 B:0LI601 4.2 37.9 1.0
CG1 B:VAL405 4.4 29.7 1.0
CB B:ASP407 4.5 51.2 1.0
C21 B:0LI601 4.5 38.5 1.0
CG B:HIS387 4.6 36.4 1.0
C B:ALA406 4.6 42.6 1.0
O B:ALA406 4.6 36.3 1.0
C13 B:0LI601 4.6 38.5 1.0
C23 B:0LI601 4.8 41.7 1.0
CD2 B:LEU325 4.8 48.2 1.0
CA B:ALA406 4.9 41.6 1.0
C14 B:0LI601 4.9 36.3 1.0
N B:ASP407 4.9 48.7 1.0
OD2 B:ASP407 5.0 53.4 1.0

Reference:

P.Soriano-Maldonado, H.N.Cuesta-Hernandez, I.Plaza-Menacho. Src Kinase Domain in Complex with Ponatinib To Be Published.
Page generated: Tue Jul 15 22:37:48 2025

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