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Fluorine in PDB 5j5s: Src Kinase in Complex with A Sulfonamide Inhibitor

Enzymatic activity of Src Kinase in Complex with A Sulfonamide Inhibitor

All present enzymatic activity of Src Kinase in Complex with A Sulfonamide Inhibitor:
2.7.10.2;

Protein crystallography data

The structure of Src Kinase in Complex with A Sulfonamide Inhibitor, PDB code: 5j5s was solved by I.Lebedev, H.C.Feldman, G.Georghiou, D.J.Maly, M.Seeliger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.24 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.210, 63.551, 73.664, 100.60, 90.61, 90.96
R / Rfree (%) 16.7 / 21.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Src Kinase in Complex with A Sulfonamide Inhibitor (pdb code 5j5s). 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 in Complex with A Sulfonamide Inhibitor, PDB code: 5j5s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5j5s

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Fluorine binding site 1 out of 6 in the Src Kinase in Complex with A Sulfonamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Src Kinase in Complex with A Sulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.5
occ:0.94
 F35 A:6G3601 0.0 0.5 0.9
C34 A:6G3601 1.3 0.9 0.9
F37 A:6G3601 2.2 0.5 0.9
F36 A:6G3601 2.2 0.8 0.9
C32 A:6G3601 2.3 76.7 0.9
C33 A:6G3601 2.6 71.0 0.9
CD2 A:PHE278 3.2 0.9 1.0
CD1 A:ILE336 3.2 69.8 1.0
CB A:PHE278 3.4 0.7 1.0
CG A:PHE278 3.5 0.2 1.0
CD2 A:LEU297 3.5 70.3 1.0
C31 A:6G3601 3.6 73.7 0.9
CD1 A:LEU297 3.6 60.7 1.0
C28 A:6G3601 4.0 65.0 0.9
CE2 A:PHE278 4.1 0.5 1.0
CG A:LEU297 4.1 78.5 1.0
O26 A:6G3601 4.3 52.1 0.9
CD A:LYS295 4.3 63.6 1.0
SD A:MET302 4.4 0.0 1.0
CD1 A:PHE278 4.5 0.5 1.0
CG1 A:ILE336 4.6 46.9 1.0
C30 A:6G3601 4.7 83.6 0.9
CA A:PHE278 4.8 0.0 1.0
C29 A:6G3601 4.9 82.8 0.9
N27 A:6G3601 4.9 65.9 0.9
CZ A:PHE278 5.0 0.4 1.0

Fluorine binding site 2 out of 6 in 5j5s

Go back to Fluorine Binding Sites List in 5j5s
Fluorine binding site 2 out of 6 in the Src Kinase in Complex with A Sulfonamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Src Kinase in Complex with A Sulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.8
occ:0.94
 F36 A:6G3601 0.0 0.8 0.9
C34 A:6G3601 1.3 0.9 0.9
F37 A:6G3601 2.2 0.5 0.9
F35 A:6G3601 2.2 0.5 0.9
C32 A:6G3601 2.3 76.7 0.9
C31 A:6G3601 2.8 73.7 0.9
CD1 A:LEU297 3.0 60.7 1.0
CD1 A:PHE307 3.1 88.8 1.0
SD A:MET302 3.4 0.0 1.0
C33 A:6G3601 3.4 71.0 0.9
CE1 A:PHE307 3.5 86.9 1.0
CD1 A:ILE336 3.5 69.8 1.0
CE A:MET302 3.6 91.4 1.0
C30 A:6G3601 4.2 83.6 0.9
CG A:LEU297 4.2 78.5 1.0
CD2 A:LEU297 4.3 70.3 1.0
CG A:PHE307 4.4 92.0 1.0
C28 A:6G3601 4.5 65.0 0.9
CG1 A:ILE336 4.5 46.9 1.0
CB A:PHE307 4.8 99.9 1.0
CZ A:PHE307 4.8 88.0 1.0
C29 A:6G3601 4.9 82.8 0.9
CD2 A:PHE278 4.9 0.9 1.0

Fluorine binding site 3 out of 6 in 5j5s

Go back to Fluorine Binding Sites List in 5j5s
Fluorine binding site 3 out of 6 in the Src Kinase in Complex with A Sulfonamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Src Kinase in Complex with A Sulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.5
occ:0.94
 F37 A:6G3601 0.0 0.5 0.9
C34 A:6G3601 1.3 0.9 0.9
F36 A:6G3601 2.2 0.8 0.9
F35 A:6G3601 2.2 0.5 0.9
C32 A:6G3601 2.3 76.7 0.9
C31 A:6G3601 2.9 73.7 0.9
SD A:MET302 3.1 0.0 1.0
CD2 A:PHE278 3.2 0.9 1.0
CG A:PHE278 3.3 0.2 1.0
C33 A:6G3601 3.4 71.0 0.9
CE2 A:PHE278 3.5 0.5 1.0
CE A:MET302 3.5 91.4 1.0
CD1 A:PHE278 3.7 0.5 1.0
CZ A:PHE278 3.9 0.4 1.0
CB A:PHE278 3.9 0.7 1.0
CE1 A:PHE278 4.0 0.7 1.0
C30 A:6G3601 4.2 83.6 0.9
CD1 A:LEU297 4.4 60.7 1.0
C28 A:6G3601 4.5 65.0 0.9
CG A:MET302 4.9 0.0 1.0
C29 A:6G3601 4.9 82.8 0.9
CD2 A:LEU297 5.0 70.3 1.0

Fluorine binding site 4 out of 6 in 5j5s

Go back to Fluorine Binding Sites List in 5j5s
Fluorine binding site 4 out of 6 in the Src Kinase in Complex with A Sulfonamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Src Kinase in Complex with A Sulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:0.9
occ:0.82
 F35 B:6G3601 0.0 0.9 0.8
C34 B:6G3601 1.3 0.1 0.8
F37 B:6G3601 2.2 0.7 0.8
F36 B:6G3601 2.2 0.2 0.8
C32 B:6G3601 2.3 0.8 0.8
C33 B:6G3601 2.7 0.1 0.8
CD B:LYS295 3.5 68.8 1.0
C31 B:6G3601 3.6 90.4 0.8
NZ B:LYS295 3.8 66.5 1.0
O26 B:6G3601 4.0 62.7 0.8
C28 B:6G3601 4.0 83.7 0.8
CD2 B:LEU297 4.1 71.3 1.0
CE B:LYS295 4.2 72.9 1.0
C30 B:6G3601 4.7 76.4 0.8
CG B:LYS295 4.8 68.7 1.0
C25 B:6G3601 4.8 60.9 0.8
CD1 B:ILE336 4.9 72.1 1.0
N27 B:6G3601 4.9 65.2 0.8
C29 B:6G3601 4.9 71.3 0.8
OD1 B:ASP404 4.9 70.5 1.0

Fluorine binding site 5 out of 6 in 5j5s

Go back to Fluorine Binding Sites List in 5j5s
Fluorine binding site 5 out of 6 in the Src Kinase in Complex with A Sulfonamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Src Kinase in Complex with A Sulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:0.2
occ:0.82
 F36 B:6G3601 0.0 0.2 0.8
C34 B:6G3601 1.3 0.1 0.8
F35 B:6G3601 2.2 0.9 0.8
F37 B:6G3601 2.2 0.7 0.8
C32 B:6G3601 2.3 0.8 0.8
C31 B:6G3601 2.9 90.4 0.8
CD2 B:LEU297 3.2 71.3 1.0
CD1 B:LEU297 3.3 70.6 1.0
C33 B:6G3601 3.5 0.1 0.8
CG B:LEU297 3.9 81.6 1.0
C30 B:6G3601 4.2 76.4 0.8
SD B:MET302 4.4 0.6 1.0
CD1 B:ILE336 4.6 72.1 1.0
C28 B:6G3601 4.7 83.7 0.8
CD B:LYS295 4.9 68.8 1.0
C29 B:6G3601 5.0 71.3 0.8

Fluorine binding site 6 out of 6 in 5j5s

Go back to Fluorine Binding Sites List in 5j5s
Fluorine binding site 6 out of 6 in the Src Kinase in Complex with A Sulfonamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Src Kinase in Complex with A Sulfonamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:0.7
occ:0.82
 F37 B:6G3601 0.0 0.7 0.8
C34 B:6G3601 1.3 0.1 0.8
F35 B:6G3601 2.2 0.9 0.8
F36 B:6G3601 2.2 0.2 0.8
C32 B:6G3601 2.3 0.8 0.8
C31 B:6G3601 3.1 90.4 0.8
C33 B:6G3601 3.3 0.1 0.8
C30 B:6G3601 4.4 76.4 0.8
C28 B:6G3601 4.5 83.7 0.8
C29 B:6G3601 4.9 71.3 0.8

Reference:

H.C.Feldman, M.Tong, L.Wang, R.Meza-Acevedo, T.A.Gobillot, M.J.Gliedt, S.B.Hari, A.K.Mitra, B.J.Backes, F.R.Papa, M.A.Seeliger, D.J.Maly. Structural and Functional Analysis of the Allosteric Modulation of IRE1A with Atp-Competitive Kinase Inhibitors To Be Published.
Page generated: Thu Aug 1 10:24:01 2024

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