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Fluorine in PDB 8b5y: SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor

Enzymatic activity of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor

All present enzymatic activity of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor:
3.1.3.48;

Protein crystallography data

The structure of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor, PDB code: 8b5y was solved by E.Torrente, A.Petrocchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.13 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.908, 190.263, 57.297, 90, 90, 90
R / Rfree (%) 17.7 / 21.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor (pdb code 8b5y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor, PDB code: 8b5y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8b5y

Go back to Fluorine Binding Sites List in 8b5y
Fluorine binding site 1 out of 6 in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:25.4
occ:1.00
 F1 A:P8O601 0.0 25.4 1.0
C2 A:P8O601 1.4 27.1 1.0
F4 A:P8O601 2.3 32.4 1.0
F3 A:P8O601 2.3 30.1 1.0
C5 A:P8O601 2.4 24.0 1.0
S11 A:P8O601 2.9 22.9 1.0
C10 A:P8O601 2.9 21.2 1.0
CD1 A:LEU254 3.4 20.2 1.0
N6 A:P8O601 3.4 25.2 1.0
CG A:GLN257 3.6 24.9 1.0
CB A:GLN495 3.6 20.3 1.0
CG A:GLN495 3.7 22.0 1.0
CD A:GLN495 3.9 22.6 1.0
CB A:GLN257 4.0 24.9 1.0
OE1 A:GLN495 4.0 23.2 1.0
C9 A:P8O601 4.3 22.7 1.0
O A:PRO491 4.3 19.3 1.0
NE2 A:GLN495 4.4 23.2 1.0
C7 A:P8O601 4.6 27.9 1.0
C12 A:P8O601 4.7 22.1 1.0
CA A:LEU254 4.7 21.0 1.0
CG A:LEU254 4.7 19.4 1.0
C A:PRO491 4.8 20.1 1.0
CD A:GLN257 4.8 27.5 1.0
O A:LEU254 4.8 19.9 1.0
C8 A:P8O601 4.9 25.0 1.0
CB A:LEU254 5.0 20.5 1.0
CA A:GLN495 5.0 20.2 1.0

Fluorine binding site 2 out of 6 in 8b5y

Go back to Fluorine Binding Sites List in 8b5y
Fluorine binding site 2 out of 6 in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:30.1
occ:1.00
 F3 A:P8O601 0.0 30.1 1.0
C2 A:P8O601 1.4 27.1 1.0
F4 A:P8O601 2.2 32.4 1.0
F1 A:P8O601 2.3 25.4 1.0
C5 A:P8O601 2.4 24.0 1.0
O A:HOH1021 3.1 41.0 1.0
NH1 A:ARG111 3.1 34.8 1.0
C10 A:P8O601 3.2 21.2 1.0
N6 A:P8O601 3.3 25.2 1.0
CG A:GLN257 3.4 24.9 1.0
S11 A:P8O601 3.5 22.9 1.0
CZ A:ARG111 3.5 33.9 1.0
CD A:ARG111 3.5 31.7 1.0
NE A:ARG111 3.6 32.2 1.0
CD A:GLN257 3.9 27.5 1.0
OE1 A:GLN257 4.0 27.9 1.0
CB A:GLN257 4.2 24.9 1.0
NH2 A:ARG111 4.4 31.9 1.0
C7 A:P8O601 4.4 27.9 1.0
C9 A:P8O601 4.4 22.7 1.0
O A:HOH1045 4.8 54.3 1.0
NE2 A:GLN257 4.8 30.5 1.0
O A:HOH1000 4.9 40.3 1.0
C12 A:P8O601 4.9 22.1 1.0
C8 A:P8O601 4.9 25.0 1.0
CG A:ARG111 5.0 30.0 1.0

Fluorine binding site 3 out of 6 in 8b5y

Go back to Fluorine Binding Sites List in 8b5y
Fluorine binding site 3 out of 6 in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:32.4
occ:1.00
 F4 A:P8O601 0.0 32.4 1.0
C2 A:P8O601 1.4 27.1 1.0
F3 A:P8O601 2.2 30.1 1.0
F1 A:P8O601 2.3 25.4 1.0
C5 A:P8O601 2.4 24.0 1.0
N6 A:P8O601 2.6 25.2 1.0
O A:HOH1045 3.0 54.3 1.0
CG A:GLN495 3.5 22.0 1.0
C10 A:P8O601 3.7 21.2 1.0
CB A:GLN495 3.7 20.3 1.0
C7 A:P8O601 3.9 27.9 1.0
O A:HOH885 4.1 27.6 1.0
CD A:GLN495 4.2 22.6 1.0
O A:HOH994 4.4 35.0 1.0
NE2 A:GLN495 4.5 23.2 1.0
S11 A:P8O601 4.6 22.9 1.0
NH1 A:ARG111 4.6 34.8 1.0
O A:HOH1021 4.7 41.0 1.0
C9 A:P8O601 4.8 22.7 1.0
C8 A:P8O601 4.9 25.0 1.0
OE1 A:GLN495 4.9 23.2 1.0
CA A:LYS492 4.9 24.4 1.0
CG A:GLN257 4.9 24.9 1.0

Fluorine binding site 4 out of 6 in 8b5y

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Fluorine binding site 4 out of 6 in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:32.4
occ:1.00
 F1 B:P8O601 0.0 32.4 1.0
C2 B:P8O601 1.4 29.6 1.0
F3 B:P8O601 2.2 33.0 1.0
F4 B:P8O601 2.3 28.6 1.0
C5 B:P8O601 2.4 28.1 1.0
N6 B:P8O601 2.6 27.4 1.0
O B:HOH982 2.9 48.4 1.0
CG B:GLN495 3.5 21.4 1.0
CB B:GLN495 3.7 21.1 1.0
C10 B:P8O601 3.7 22.3 1.0
C7 B:P8O601 3.9 28.5 1.0
O B:HOH906 4.1 29.2 1.0
CD B:GLN495 4.1 22.0 1.0
O B:HOH986 4.3 34.4 1.0
NE2 B:GLN495 4.4 22.6 1.0
S11 B:P8O601 4.6 22.1 1.0
O B:HOH994 4.6 40.0 1.0
NH1 B:ARG111 4.6 34.4 1.0
C9 B:P8O601 4.8 23.1 1.0
C8 B:P8O601 4.9 25.0 1.0
OE1 B:GLN495 4.9 22.8 1.0
CG B:GLN257 4.9 25.9 1.0
CA B:LYS492 5.0 24.8 1.0

Fluorine binding site 5 out of 6 in 8b5y

Go back to Fluorine Binding Sites List in 8b5y
Fluorine binding site 5 out of 6 in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:33.0
occ:1.00
 F3 B:P8O601 0.0 33.0 1.0
C2 B:P8O601 1.4 29.6 1.0
F1 B:P8O601 2.2 32.4 1.0
F4 B:P8O601 2.3 28.6 1.0
C5 B:P8O601 2.4 28.1 1.0
O B:HOH994 2.9 40.0 1.0
NH1 B:ARG111 3.2 34.4 1.0
C10 B:P8O601 3.2 22.3 1.0
N6 B:P8O601 3.2 27.4 1.0
CD B:ARG111 3.4 30.8 1.0
CG B:GLN257 3.5 25.9 1.0
CZ B:ARG111 3.5 34.0 1.0
S11 B:P8O601 3.6 22.1 1.0
NE B:ARG111 3.6 31.6 1.0
CD B:GLN257 3.9 28.2 1.0
OE1 B:GLN257 4.0 28.3 1.0
CB B:GLN257 4.2 25.1 1.0
NH2 B:ARG111 4.4 32.4 1.0
C7 B:P8O601 4.4 28.5 1.0
C9 B:P8O601 4.5 23.1 1.0
O B:HOH982 4.6 48.4 1.0
O B:HOH942 4.9 40.2 1.0
NE2 B:GLN257 4.9 31.1 1.0
CG B:ARG111 4.9 29.4 1.0
C8 B:P8O601 5.0 25.0 1.0
C12 B:P8O601 5.0 23.1 1.0

Fluorine binding site 6 out of 6 in 8b5y

Go back to Fluorine Binding Sites List in 8b5y
Fluorine binding site 6 out of 6 in the SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of SHP2 in Complex with Allosteric Imidazopyrazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:28.6
occ:1.00
 F4 B:P8O601 0.0 28.6 1.0
C2 B:P8O601 1.4 29.6 1.0
F1 B:P8O601 2.3 32.4 1.0
F3 B:P8O601 2.3 33.0 1.0
C5 B:P8O601 2.4 28.1 1.0
S11 B:P8O601 2.9 22.1 1.0
C10 B:P8O601 2.9 22.3 1.0
CD1 B:LEU254 3.4 20.8 1.0
N6 B:P8O601 3.5 27.4 1.0
CG B:GLN257 3.6 25.9 1.0
CB B:GLN495 3.7 21.1 1.0
CG B:GLN495 3.8 21.4 1.0
CD B:GLN495 3.9 22.0 1.0
CB B:GLN257 4.0 25.1 1.0
OE1 B:GLN495 4.0 22.8 1.0
C9 B:P8O601 4.2 23.1 1.0
O B:PRO491 4.3 19.5 1.0
NE2 B:GLN495 4.4 22.6 1.0
C7 B:P8O601 4.6 28.5 1.0
CA B:LEU254 4.6 20.6 1.0
C12 B:P8O601 4.6 23.1 1.0
O B:LEU254 4.7 20.2 1.0
CD B:GLN257 4.7 28.2 1.0
CG B:LEU254 4.7 19.9 1.0
C B:PRO491 4.8 21.6 1.0
O B:HOH982 4.9 48.4 1.0
C8 B:P8O601 4.9 25.0 1.0
CB B:LEU254 5.0 19.9 1.0
CD B:ARG111 5.0 30.8 1.0

Reference:

E.Torrente, V.Fodale, A.Ciammaichella, F.Ferrigno, J.Ontoria, S.Ponzi, I.Rossetti, A.Sferrazza, J.Amaudrut, A.Missineo, S.Esposito, S.Palombo, M.Nibbio, M.Cerretani, M.Bisbocci, A.Cellucci, A.Di Marco, C.Alli, V.Pucci, C.Toniatti, A.Petrocchi. Discovery of A Novel Series of Imidazopyrazine Derivatives As Potent SHP2 Allosteric Inhibitors To Be Published.
Page generated: Wed Jul 16 02:48:49 2025

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