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Fluorine in PDB 8tdu: Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA

Enzymatic activity of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA

All present enzymatic activity of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA:
2.7.1.137; 2.7.1.153; 2.7.11.1;

Protein crystallography data

The structure of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA, PDB code: 8tdu was solved by B.J.Hilbert, N.Brooijmans, L.Buckbinder, D.J.St.Jean Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.77 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.34, 124.72, 165.84, 90, 92.8, 90
R / Rfree (%) 20.8 / 26.7

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Fluorine atom in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA (pdb code 8tdu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 14 binding sites of Fluorine where determined in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA, PDB code: 8tdu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 14 in 8tdu

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Fluorine binding site 1 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:78.2
occ:1.00
 F30 A:X3N1101 0.0 78.2 1.0
C29 A:X3N1101 1.4 71.8 1.0
F31 A:X3N1101 2.3 73.7 1.0
C23 A:X3N1101 2.4 63.9 1.0
C25 A:X3N1101 2.8 64.6 1.0
CB A:SER774 3.1 73.5 1.0
OG A:SER774 3.3 68.1 1.0
CG A:PRO778 3.6 63.8 1.0
N22 A:X3N1101 3.7 59.4 1.0
CE A:MET772 3.8 70.6 1.0
O26 A:X3N1101 4.1 64.1 1.0
SD A:MET772 4.3 68.9 1.0
CD A:PRO778 4.4 64.1 1.0
C27 A:X3N1101 4.4 63.7 1.0
N19 A:X3N1101 4.5 61.9 1.0
C20 A:X3N1101 4.5 59.1 1.0
CA A:SER774 4.6 72.5 1.0
CE A:LYS802 4.7 62.6 1.0
O A:HOH1209 4.7 49.0 1.0
CB A:PRO778 4.8 63.1 1.0
CG2 A:ILE800 4.8 51.8 1.0
CB A:MET772 4.9 66.8 1.0
CD1 A:ILE800 4.9 50.5 1.0

Fluorine binding site 2 out of 14 in 8tdu

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Fluorine binding site 2 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:73.7
occ:1.00
 F31 A:X3N1101 0.0 73.7 1.0
C29 A:X3N1101 1.4 71.8 1.0
F30 A:X3N1101 2.3 78.2 1.0
C23 A:X3N1101 2.4 63.9 1.0
N22 A:X3N1101 2.9 59.4 1.0
C25 A:X3N1101 2.9 64.6 1.0
C27 A:X3N1101 3.4 63.7 1.0
O26 A:X3N1101 3.4 64.1 1.0
CG2 A:ILE800 3.5 51.8 1.0
C20 A:X3N1101 3.6 59.1 1.0
CE A:LYS802 3.6 62.6 1.0
CD1 A:ILE800 3.9 50.5 1.0
N19 A:X3N1101 4.0 61.9 1.0
CG A:PRO778 4.2 63.8 1.0
NZ A:LYS802 4.2 65.5 1.0
O28 A:X3N1101 4.3 71.8 1.0
CD1 A:ILE848 4.4 71.9 1.0
CB A:ILE800 4.4 51.9 1.0
C21 A:X3N1101 4.6 60.0 1.0
CE A:MET772 4.7 70.6 1.0
CG1 A:ILE800 4.7 50.3 1.0
CB A:PRO778 4.8 63.1 1.0
CG1 A:ILE848 4.8 63.2 1.0
SD A:MET772 4.8 68.9 1.0
CD A:LYS802 5.0 59.5 1.0

Fluorine binding site 3 out of 14 in 8tdu

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Fluorine binding site 3 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:55.6
occ:1.00
 F1 A:ZWE1102 0.0 55.6 1.0
C5 A:ZWE1102 1.3 51.9 1.0
C4 A:ZWE1102 2.3 53.2 1.0
C6 A:ZWE1102 2.4 52.8 1.0
O1 A:ZWE1102 2.9 55.9 1.0
OG1 A:THR813 3.5 50.1 1.0
C9 A:ZWE1102 3.6 55.2 1.0
C7 A:ZWE1102 3.6 55.8 1.0
CZ A:PHE937 3.7 59.4 1.0
CZ A:PHE1002 3.7 60.0 1.0
CD1 A:LEU911 3.8 57.6 1.0
CE1 A:PHE1002 3.9 59.3 1.0
CD2 A:LEU911 4.1 52.9 1.0
C8 A:ZWE1102 4.1 55.7 1.0
C3 A:ZWE1102 4.2 57.2 1.0
CA A:THR813 4.2 50.7 1.0
CB A:THR813 4.3 50.4 1.0
CG A:LEU911 4.3 54.4 1.0
CE2 A:PHE937 4.4 59.5 1.0
CG2 A:THR813 4.5 49.1 1.0
CB A:LEU911 4.5 56.5 1.0
C2 A:ZWE1102 4.6 59.1 1.0
F3 A:ZWE1102 4.6 62.6 1.0
CE1 A:PHE937 4.7 58.9 1.0
F2 A:ZWE1102 4.8 64.9 1.0
N A:THR813 4.8 51.7 1.0
CG1 A:ILE816 4.9 54.1 1.0
CE2 A:PHE1002 5.0 60.7 1.0

Fluorine binding site 4 out of 14 in 8tdu

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Fluorine binding site 4 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:64.9
occ:1.00
 F2 A:ZWE1102 0.0 64.9 1.0
C7 A:ZWE1102 1.4 55.8 1.0
C8 A:ZWE1102 2.4 55.7 1.0
C6 A:ZWE1102 2.4 52.8 1.0
CD2 A:LEU812 3.4 60.6 1.0
C5 A:ZWE1102 3.6 51.9 1.0
C9 A:ZWE1102 3.6 55.2 1.0
CG A:GLN809 3.7 58.3 1.0
CA A:GLN809 3.8 60.1 1.0
CB A:LEU812 4.0 55.5 1.0
CG A:LEU812 4.0 58.1 1.0
CB A:GLN809 4.0 61.6 1.0
CD1 A:LEU1013 4.1 75.9 1.0
O A:GLN809 4.1 51.4 1.0
C4 A:ZWE1102 4.1 53.2 1.0
CD A:GLN809 4.4 63.7 1.0
C A:GLN809 4.4 57.2 1.0
CG A:LEU1013 4.4 73.6 1.0
SD A:MET1010 4.5 70.1 1.0
CG A:GLU1012 4.6 77.2 1.0
OG1 A:THR813 4.7 50.1 1.0
F1 A:ZWE1102 4.8 55.6 1.0
N A:GLN809 4.8 60.5 1.0
O A:ARG808 4.9 58.7 1.0
OE1 A:GLN809 4.9 66.0 1.0
CD1 A:LEU938 5.0 65.2 1.0

Fluorine binding site 5 out of 14 in 8tdu

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Fluorine binding site 5 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:62.6
occ:1.00
 F3 A:ZWE1102 0.0 62.6 1.0
C16 A:ZWE1102 1.4 61.1 1.0
F5 A:ZWE1102 2.2 59.0 1.0
F4 A:ZWE1102 2.3 62.1 1.0
C10 A:ZWE1102 2.4 59.2 1.0
O1 A:ZWE1102 2.7 55.9 1.0
N1 A:ZWE1102 2.9 59.9 1.0
C3 A:ZWE1102 2.9 57.2 1.0
CD2 A:LEU911 3.3 52.9 1.0
CA A:LEU911 3.6 58.2 1.0
O A:LEU911 3.6 61.0 1.0
C4 A:ZWE1102 3.9 53.2 1.0
C A:LEU911 4.0 58.6 1.0
CZ A:PHE1002 4.0 60.0 1.0
CE2 A:PHE1002 4.0 60.7 1.0
CB A:LEU911 4.1 56.5 1.0
C11 A:ZWE1102 4.1 62.4 1.0
C2 A:ZWE1102 4.1 59.1 1.0
O A:ILE910 4.3 65.2 1.0
CB A:ILE1022 4.3 63.5 1.0
CG A:LEU911 4.3 54.4 1.0
CD1 A:ILE1022 4.4 68.2 1.0
CG1 A:ILE1022 4.6 66.3 1.0
F1 A:ZWE1102 4.6 55.6 1.0
N A:LEU911 4.7 56.4 1.0
C9 A:ZWE1102 4.7 55.2 1.0
C5 A:ZWE1102 4.8 51.9 1.0
O2 A:ZWE1102 4.8 68.3 1.0
C A:ILE910 4.9 56.9 1.0
CE1 A:PHE1002 4.9 59.3 1.0
CD2 A:PHE1002 4.9 61.0 1.0
N2 A:ZWE1102 4.9 64.5 1.0

Fluorine binding site 6 out of 14 in 8tdu

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Fluorine binding site 6 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:62.1
occ:1.00
 F4 A:ZWE1102 0.0 62.1 1.0
C16 A:ZWE1102 1.4 61.1 1.0
F3 A:ZWE1102 2.3 62.6 1.0
F5 A:ZWE1102 2.3 59.0 1.0
C10 A:ZWE1102 2.4 59.2 1.0
C3 A:ZWE1102 2.9 57.2 1.0
O1 A:ZWE1102 3.4 55.9 1.0
CE2 A:PHE1002 3.6 60.7 1.0
C2 A:ZWE1102 3.7 59.1 1.0
N1 A:ZWE1102 3.7 59.9 1.0
O A:ILE1019 3.7 80.4 1.0
CA A:ILE1019 3.8 74.7 1.0
CD2 A:PHE1002 3.9 61.0 1.0
CZ A:PHE1002 4.0 60.0 1.0
CG2 A:ILE1019 4.0 77.0 1.0
CB A:ILE1022 4.1 63.5 1.0
C A:ILE1019 4.2 79.4 1.0
C1 A:ZWE1102 4.3 66.6 1.0
C4 A:ZWE1102 4.4 53.2 1.0
O A:ASP1018 4.4 83.3 1.0
CB A:ILE1019 4.4 72.8 1.0
CG2 A:ILE1022 4.4 64.9 1.0
CG A:PHE1002 4.4 63.6 1.0
CE1 A:PHE1002 4.5 59.3 1.0
C9 A:ZWE1102 4.6 55.2 1.0
CD1 A:ILE1022 4.7 68.2 1.0
N A:ILE1022 4.7 65.8 1.0
CD1 A:PHE1002 4.7 61.5 1.0
C11 A:ZWE1102 4.8 62.4 1.0
CG1 A:ILE1019 4.8 78.4 1.0
N A:ILE1019 4.8 79.5 1.0
CG1 A:ILE1022 4.9 66.3 1.0
CA A:ILE1022 4.9 63.0 1.0
O2 A:ZWE1102 4.9 68.3 1.0
C A:ASP1018 5.0 86.2 1.0

Fluorine binding site 7 out of 14 in 8tdu

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Fluorine binding site 7 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:59.0
occ:1.00
 F5 A:ZWE1102 0.0 59.0 1.0
C16 A:ZWE1102 1.4 61.1 1.0
F3 A:ZWE1102 2.2 62.6 1.0
F4 A:ZWE1102 2.3 62.1 1.0
C10 A:ZWE1102 2.4 59.2 1.0
N1 A:ZWE1102 2.8 59.9 1.0
N A:ILE1022 3.2 65.8 1.0
CB A:ILE1022 3.4 63.5 1.0
C11 A:ZWE1102 3.5 62.4 1.0
CA A:ILE1022 3.6 63.0 1.0
CD2 A:TYR1021 3.6 79.4 1.0
CB A:TYR1021 3.7 68.1 1.0
C3 A:ZWE1102 3.7 57.2 1.0
O A:ILE1019 3.7 80.4 1.0
O2 A:ZWE1102 3.7 68.3 1.0
C A:TYR1021 3.9 66.0 1.0
CG A:TYR1021 4.1 70.0 1.0
O1 A:ZWE1102 4.2 55.9 1.0
CA A:TYR1021 4.2 67.1 1.0
O A:ILE910 4.3 65.2 1.0
CG1 A:ILE1022 4.3 66.3 1.0
O A:LEU911 4.3 61.0 1.0
CG2 A:ILE1022 4.4 64.9 1.0
N2 A:ZWE1102 4.5 64.5 1.0
C A:ILE1019 4.5 79.4 1.0
N A:TYR1021 4.5 66.5 1.0
O A:ASP1018 4.6 83.3 1.0
CE2 A:TYR1021 4.7 80.6 1.0
C A:LEU911 4.7 58.6 1.0
O A:TYR1021 4.7 68.1 1.0
CA A:LEU911 4.7 58.2 1.0
CD1 A:ILE1022 4.8 68.2 1.0
C2 A:ZWE1102 4.8 59.1 1.0
CA A:ILE1019 4.8 74.7 1.0

Fluorine binding site 8 out of 14 in 8tdu

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Fluorine binding site 8 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:78.7
occ:1.00
 F30 C:X3N1101 0.0 78.7 1.0
C29 C:X3N1101 1.4 79.7 1.0
F31 C:X3N1101 2.3 83.9 1.0
C23 C:X3N1101 2.4 80.1 1.0
N22 C:X3N1101 2.6 83.9 1.0
C27 C:X3N1101 3.1 91.4 1.0
C25 C:X3N1101 3.2 82.5 1.0
O26 C:X3N1101 3.2 85.7 1.0
C20 C:X3N1101 3.3 85.1 1.0
N19 C:X3N1101 3.7 84.2 1.0
CG2 C:ILE800 3.8 69.2 1.0
CE C:LYS802 3.8 109.9 1.0
O28 C:X3N1101 3.9 101.8 1.0
NZ C:LYS802 4.0 106.7 1.0
CD1 C:ILE800 4.1 74.3 1.0
C21 C:X3N1101 4.3 86.8 1.0
CD1 C:ILE848 4.3 86.4 1.0
CG C:PRO778 4.6 84.8 1.0
CB C:ILE800 4.6 68.5 1.0
CG1 C:ILE848 4.7 78.3 1.0
CD C:LYS802 4.7 102.1 1.0
C18 C:X3N1101 4.8 81.0 1.0
CG1 C:ILE800 4.9 73.2 1.0
CB C:ILE848 5.0 75.7 1.0

Fluorine binding site 9 out of 14 in 8tdu

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Fluorine binding site 9 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:83.9
occ:1.00
 F31 C:X3N1101 0.0 83.9 1.0
C29 C:X3N1101 1.4 79.7 1.0
F30 C:X3N1101 2.3 78.7 1.0
C23 C:X3N1101 2.3 80.1 1.0
N19 C:X3N1101 3.1 84.2 1.0
N22 C:X3N1101 3.1 83.9 1.0
C20 C:X3N1101 3.4 85.1 1.0
CE C:MET772 3.5 81.7 1.0
C25 C:X3N1101 3.6 82.5 1.0
SD C:MET772 3.9 88.3 1.0
OG C:SER774 3.9 100.3 1.0
CD1 C:ILE800 4.0 74.3 1.0
CB C:SER774 4.2 98.4 1.0
C18 C:X3N1101 4.2 81.0 1.0
C27 C:X3N1101 4.2 91.4 1.0
C10 C:X3N1101 4.4 79.4 1.0
O26 C:X3N1101 4.4 85.7 1.0
CG C:PRO778 4.5 84.8 1.0
CG2 C:ILE800 4.6 69.2 1.0
C21 C:X3N1101 4.7 86.8 1.0
C11 C:X3N1101 4.8 79.0 1.0
CG1 C:ILE800 5.0 73.2 1.0

Fluorine binding site 10 out of 14 in 8tdu

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Fluorine binding site 10 out of 14 in the Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Stx-478, A Mutant-Selective, Allosteric Inhibitor Bound to PI3KALPHA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1102

b:89.5
occ:1.00
 F1 C:ZWE1102 0.0 89.5 1.0
C5 C:ZWE1102 1.4 94.1 1.0
C4 C:ZWE1102 2.3 93.9 1.0
C6 C:ZWE1102 2.4 93.6 1.0
O1 C:ZWE1102 2.9 101.3 1.0
CD1 C:LEU911 3.5 90.7 1.0
CZ C:PHE937 3.5 85.5 1.0
C9 C:ZWE1102 3.6 93.6 1.0
C7 C:ZWE1102 3.7 90.2 1.0
CB C:THR813 3.7 68.4 1.0
CD2 C:LEU911 3.8 83.3 1.0
CG C:LEU911 4.0 86.6 1.0
CZ C:PHE1002 4.1 65.3 1.0
OG1 C:THR813 4.1 67.2 1.0
CB C:LEU911 4.1 90.0 1.0
C8 C:ZWE1102 4.2 87.8 1.0
CA C:THR813 4.2 65.9 1.0
C3 C:ZWE1102 4.2 98.0 1.0
CE2 C:PHE937 4.3 84.6 1.0
CE1 C:PHE1002 4.3 68.7 1.0
CE1 C:PHE937 4.5 87.7 1.0
C2 C:ZWE1102 4.6 98.5 1.0
F5 C:ZWE1102 4.7 87.5 1.0
F2 C:ZWE1102 4.8 98.7 1.0
CG2 C:THR813 4.9 74.8 1.0
N C:THR813 4.9 61.6 1.0

Reference:

L.Buckbinder, D.J.St Jean, T.Tieu, B.Ladd, B.Hilbert, W.Wang, J.T.Alltucker, S.Manimala, G.V.Kryukov, N.Brooijmans, G.Dowdell, P.Jonsson, M.Huff, A.Guzman-Perez, E.L.Jackson, M.D.Goncalves, D.D.Stuart. Stx-478, A Mutant-Selective, Allosteric PI3KA Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3KA-Mutant Xenografts. Cancer Discov 2023.
ISSN: ESSN 2159-8290
PubMed: 37623743
DOI: 10.1158/2159-8290.CD-23-0396
Page generated: Wed Jul 16 08:37:03 2025

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