Fluorine in PDB 7wf5: C-Src in Complex with Ponatinib

Enzymatic activity of C-Src in Complex with Ponatinib

All present enzymatic activity of C-Src in Complex with Ponatinib:
2.7.10.2;

Protein crystallography data

The structure of C-Src in Complex with Ponatinib, PDB code: 7wf5 was solved by M.Guo, Y.Duan, S.Dai, X.Chen, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.91 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.927, 63.632, 74.505, 79.14, 89.5, 88.8
R / Rfree (%) 16.2 / 18.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the C-Src in Complex with Ponatinib (pdb code 7wf5). 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-Src in Complex with Ponatinib, PDB code: 7wf5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7wf5

Go back to Fluorine Binding Sites List in 7wf5
Fluorine binding site 1 out of 6 in the C-Src 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-Src in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:29.4
occ:1.00
 F1 A:0LI601 0.0 29.4 1.0
C19 A:0LI601 1.4 28.1 1.0
F2 A:0LI601 2.2 29.0 1.0
F3 A:0LI601 2.2 28.9 1.0
C17 A:0LI601 2.3 21.2 1.0
C20 A:0LI601 3.0 25.0 1.0
C16 A:0LI601 3.0 21.8 1.0
C18 A:0LI601 3.4 24.5 1.0
CD2 A:LEU322 3.5 22.8 1.0
CG A:LEU322 3.7 24.8 1.0
CD1 A:LEU317 3.8 42.0 1.0
C15 A:0LI601 4.3 25.9 1.0
N3 A:0LI601 4.5 26.5 1.0
CB A:LEU322 4.6 24.2 1.0
C13 A:0LI601 4.6 24.3 1.0
O A:HOH823 4.7 34.4 1.0
CG1 A:VAL402 4.8 18.2 1.0
CD1 A:LEU322 4.9 25.7 1.0
CG2 A:VAL377 4.9 21.1 1.0
O A:VAL402 4.9 18.2 1.0
C14 A:0LI601 5.0 27.1 1.0

Fluorine binding site 2 out of 6 in 7wf5

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Fluorine binding site 2 out of 6 in the C-Src 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-Src in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:29.0
occ:1.00
 F2 A:0LI601 0.0 29.0 1.0
C19 A:0LI601 1.4 28.1 1.0
F1 A:0LI601 2.2 29.4 1.0
F3 A:0LI601 2.2 28.9 1.0
C17 A:0LI601 2.3 21.2 1.0
C16 A:0LI601 3.0 21.8 1.0
C20 A:0LI601 3.0 25.0 1.0
C18 A:0LI601 3.3 24.5 1.0
CD2 A:HIS384 3.4 22.6 1.0
NE2 A:HIS384 3.7 22.9 1.0
CG1 A:VAL402 3.7 18.2 1.0
O A:ALA403 3.9 20.2 1.0
C21 A:0LI601 4.0 22.8 1.0
C A:ALA403 4.0 19.4 1.0
N3 A:0LI601 4.1 26.5 1.0
CB A:ASP404 4.2 27.4 1.0
C15 A:0LI601 4.3 25.9 1.0
CA A:ALA403 4.5 21.1 1.0
N A:ASP404 4.5 21.2 1.0
CG A:HIS384 4.5 22.6 1.0
C13 A:0LI601 4.5 24.3 1.0
N A:ALA403 4.5 17.9 1.0
C A:VAL402 4.7 19.5 1.0
CE1 A:HIS384 4.7 25.9 1.0
O A:VAL402 4.7 18.2 1.0
CB A:VAL402 4.8 18.9 1.0
C14 A:0LI601 4.9 27.1 1.0
CA A:ASP404 4.9 22.7 1.0
C24 A:0LI601 4.9 29.0 1.0

Fluorine binding site 3 out of 6 in 7wf5

Go back to Fluorine Binding Sites List in 7wf5
Fluorine binding site 3 out of 6 in the C-Src 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-Src in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:28.9
occ:1.00
 F3 A:0LI601 0.0 28.9 1.0
C19 A:0LI601 1.4 28.1 1.0
F1 A:0LI601 2.2 29.4 1.0
F2 A:0LI601 2.2 29.0 1.0
C17 A:0LI601 2.4 21.2 1.0
C18 A:0LI601 2.6 24.5 1.0
O A:VAL402 3.0 18.2 1.0
CA A:ALA403 3.5 21.1 1.0
C A:VAL402 3.5 19.5 1.0
N A:ALA403 3.7 17.9 1.0
C16 A:0LI601 3.7 21.8 1.0
C A:ALA403 3.8 19.4 1.0
CG1 A:VAL402 4.0 18.2 1.0
C13 A:0LI601 4.0 24.3 1.0
CG A:LEU322 4.1 24.8 1.0
CG1 A:VAL323 4.2 30.4 1.0
O A:ALA403 4.2 20.2 1.0
O1 A:0LI601 4.2 26.8 1.0
N A:ASP404 4.3 21.2 1.0
C20 A:0LI601 4.4 25.0 1.0
CB A:VAL402 4.4 18.9 1.0
N A:VAL323 4.5 20.7 1.0
CB A:LEU322 4.5 24.2 1.0
CA A:VAL402 4.6 16.4 1.0
CD2 A:LEU322 4.7 22.8 1.0
CA A:LEU322 4.8 19.7 1.0
C15 A:0LI601 4.8 25.9 1.0
CB A:ALA403 4.8 19.7 1.0
N2 A:0LI601 4.8 22.9 1.0
C12 A:0LI601 4.9 26.6 1.0
C14 A:0LI601 4.9 27.1 1.0
O A:VAL323 5.0 26.9 1.0

Fluorine binding site 4 out of 6 in 7wf5

Go back to Fluorine Binding Sites List in 7wf5
Fluorine binding site 4 out of 6 in the C-Src 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-Src in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:29.3
occ:1.00
 F1 B:0LI601 0.0 29.3 1.0
C19 B:0LI601 1.4 27.1 1.0
F3 B:0LI601 2.2 25.1 1.0
F2 B:0LI601 2.2 32.6 1.0
C17 B:0LI601 2.3 20.3 1.0
C16 B:0LI601 3.1 20.0 1.0
C20 B:0LI601 3.1 20.3 1.0
C18 B:0LI601 3.3 16.7 1.0
CD2 B:HIS384 3.4 18.6 1.0
CG1 B:VAL402 3.6 15.8 1.0
NE2 B:HIS384 3.6 18.2 1.0
O B:ALA403 3.9 15.1 1.0
C B:ALA403 4.0 18.1 1.0
C21 B:0LI601 4.1 18.9 1.0
N3 B:0LI601 4.2 22.4 1.0
CB B:ASP404 4.3 19.4 1.0
C15 B:0LI601 4.3 23.9 1.0
CA B:ALA403 4.4 16.9 1.0
CG B:HIS384 4.4 19.7 1.0
N B:ALA403 4.5 17.0 1.0
C13 B:0LI601 4.5 20.9 1.0
N B:ASP404 4.5 19.1 1.0
O B:VAL402 4.6 17.9 1.0
C B:VAL402 4.6 19.0 1.0
CB B:VAL402 4.7 17.7 1.0
CE1 B:HIS384 4.7 22.7 1.0
C14 B:0LI601 4.9 21.8 1.0
CA B:ASP404 4.9 17.8 1.0

Fluorine binding site 5 out of 6 in 7wf5

Go back to Fluorine Binding Sites List in 7wf5
Fluorine binding site 5 out of 6 in the C-Src 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-Src in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:32.6
occ:1.00
 F2 B:0LI601 0.0 32.6 1.0
C19 B:0LI601 1.4 27.1 1.0
F3 B:0LI601 2.2 25.1 1.0
F1 B:0LI601 2.2 29.3 1.0
C17 B:0LI601 2.4 20.3 1.0
C18 B:0LI601 2.6 16.7 1.0
O B:VAL402 3.0 17.9 1.0
C B:VAL402 3.6 19.0 1.0
CA B:ALA403 3.6 16.9 1.0
C16 B:0LI601 3.7 20.0 1.0
N B:ALA403 3.8 17.0 1.0
C B:ALA403 3.9 18.1 1.0
C13 B:0LI601 4.0 20.9 1.0
CG B:LEU322 4.0 20.2 1.0
CG1 B:VAL323 4.1 26.0 1.0
CG1 B:VAL402 4.1 15.8 1.0
O1 B:0LI601 4.2 23.8 1.0
O B:ALA403 4.4 15.1 1.0
CB B:LEU322 4.4 15.9 1.0
N B:VAL323 4.4 16.9 1.0
C20 B:0LI601 4.4 20.3 1.0
N B:ASP404 4.4 19.1 1.0
CB B:VAL402 4.5 17.7 1.0
CD2 B:LEU322 4.5 20.8 1.0
CA B:VAL402 4.6 15.5 1.0
O B:VAL323 4.8 22.7 1.0
CA B:LEU322 4.8 14.3 1.0
C15 B:0LI601 4.8 23.9 1.0
N2 B:0LI601 4.8 20.1 1.0
O B:HOH760 4.9 31.9 1.0
C12 B:0LI601 4.9 21.4 1.0
C14 B:0LI601 4.9 21.8 1.0
CB B:ALA403 4.9 15.6 1.0
C B:LEU322 5.0 16.1 1.0

Fluorine binding site 6 out of 6 in 7wf5

Go back to Fluorine Binding Sites List in 7wf5
Fluorine binding site 6 out of 6 in the C-Src 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-Src in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:25.1
occ:1.00
 F3 B:0LI601 0.0 25.1 1.0
C19 B:0LI601 1.4 27.1 1.0
F1 B:0LI601 2.2 29.3 1.0
F2 B:0LI601 2.2 32.6 1.0
C17 B:0LI601 2.3 20.3 1.0
C20 B:0LI601 3.0 20.3 1.0
C16 B:0LI601 3.0 20.0 1.0
C18 B:0LI601 3.4 16.7 1.0
CD2 B:LEU322 3.4 20.8 1.0
CD1 B:LEU317 3.7 27.8 1.0
CG B:LEU322 3.8 20.2 1.0
C15 B:0LI601 4.3 23.9 1.0
N3 B:0LI601 4.4 22.4 1.0
CB B:LEU322 4.6 15.9 1.0
C13 B:0LI601 4.6 20.9 1.0
O B:HOH760 4.7 31.9 1.0
CG2 B:VAL377 4.9 19.2 1.0
CG1 B:VAL402 4.9 15.8 1.0
C21 B:0LI601 4.9 18.9 1.0
O B:VAL402 5.0 17.9 1.0
CD1 B:LEU322 5.0 20.4 1.0
C14 B:0LI601 5.0 21.8 1.0
C24 B:0LI601 5.0 25.4 1.0

Reference:

M.Guo, Y.Duan, S.Dai, J.Li, X.Chen, L.Qu, Z.Chen, H.Wei, L.Jiang, Y.Chen. Structural Study of Ponatinib in Inhibiting Src Kinase. Biochem.Biophys.Res.Commun. V. 598 15 2022.
ISSN: ESSN 1090-2104
PubMed: 35151199
DOI: 10.1016/J.BBRC.2022.02.001
Page generated: Wed Apr 5 01:40:59 2023

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