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Fluorine in PDB 8a92: P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine

Protein crystallography data

The structure of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine, PDB code: 8a92 was solved by J.Stahlecker, M.B.Braun, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.68 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.077, 71.109, 105.226, 90, 90, 90
R / Rfree (%) 15.3 / 18.3

Other elements in 8a92:

The structure of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine also contains other interesting chemical elements:

Bromine (Br) 3 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine (pdb code 8a92). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine, PDB code: 8a92:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 8a92

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Fluorine binding site 1 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:25.8
occ:0.40
 F1 A:LE9401 0.0 25.8 0.4
C4 A:LE9401 1.1 41.6 0.4
F1 A:LE9401 1.2 41.2 0.4
F3 A:LE9401 1.3 42.0 0.4
C4 A:LE9401 1.3 29.8 0.4
C3 A:LE9401 2.0 40.4 0.4
F2 A:LE9401 2.1 32.2 0.4
F3 A:LE9401 2.1 27.5 0.4
C3 A:LE9401 2.3 33.5 0.4
F2 A:LE9401 2.3 42.9 0.4
C1 A:LE9401 2.6 39.8 0.4
N2 A:LE9401 2.7 33.5 0.4
BR1 A:LE9401 2.9 40.0 0.4
N2 A:LE9401 3.2 39.8 0.4
C1 A:LE9401 3.7 36.3 0.4
CB A:LEU145 3.7 15.5 1.0
CG1 A:VAL147 3.8 17.1 1.0
C2 A:LE9401 3.9 39.9 0.4
N1 A:LE9401 4.1 34.8 0.4
O A:LEU145 4.2 17.0 1.0
CG2 A:VAL147 4.2 17.4 1.0
N1 A:LE9401 4.2 39.5 0.4
CD1 A:LEU145 4.4 18.7 1.0
C A:LEU145 4.4 13.7 1.0
C2 A:LE9401 4.5 35.7 0.4
OG1 A:THR230 4.6 24.2 1.0
CB A:VAL147 4.6 16.2 1.0
CB A:THR230 4.7 21.0 1.0
BR1 A:LE9401 4.7 39.9 0.4
CG A:LEU145 4.7 15.7 1.0
CA A:LEU145 4.7 13.1 1.0
N A:TRP146 4.9 12.4 1.0
CD A:PRO151 5.0 18.2 1.0
N A:VAL147 5.0 14.5 1.0

Fluorine binding site 2 out of 9 in 8a92

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Fluorine binding site 2 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.2
occ:0.40
 F1 A:LE9401 0.0 41.2 0.4
F1 A:LE9401 1.2 25.8 0.4
C4 A:LE9401 1.3 41.6 0.4
F2 A:LE9401 1.5 32.2 0.4
C4 A:LE9401 1.6 29.8 0.4
F3 A:LE9401 2.1 42.0 0.4
F2 A:LE9401 2.1 42.9 0.4
C3 A:LE9401 2.3 40.4 0.4
F3 A:LE9401 2.6 27.5 0.4
C3 A:LE9401 2.7 33.5 0.4
N2 A:LE9401 3.2 39.8 0.4
C1 A:LE9401 3.3 39.8 0.4
CG1 A:VAL147 3.3 17.1 1.0
N2 A:LE9401 3.4 33.5 0.4
C1 A:LE9401 3.8 36.3 0.4
BR1 A:LE9401 3.9 40.0 0.4
CG A:PRO151 4.0 20.6 1.0
CG2 A:VAL147 4.1 17.4 1.0
CD A:PRO151 4.2 18.2 1.0
CD1 A:LEU257 4.3 15.3 1.0
CB A:VAL147 4.3 16.2 1.0
N1 A:LE9401 4.3 39.5 0.4
C2 A:LE9401 4.4 39.9 0.4
CB A:LEU145 4.4 15.5 1.0
BR1 A:LE9401 4.5 39.9 0.4
N1 A:LE9401 4.6 34.8 0.4
SG A:CYS220 4.6 27.5 0.8
C2 A:LE9401 4.8 35.7 0.4
CD1 A:LEU145 4.8 18.7 1.0
CB A:CYS220 4.9 21.8 0.8
CD1 A:PHE109 4.9 13.4 1.0
CD2 A:LEU257 5.0 16.1 1.0

Fluorine binding site 3 out of 9 in 8a92

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Fluorine binding site 3 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.2
occ:0.40
 F2 A:LE9401 0.0 32.2 0.4
F2 A:LE9401 1.0 42.9 0.4
C4 A:LE9401 1.3 41.6 0.4
C4 A:LE9401 1.3 29.8 0.4
F1 A:LE9401 1.5 41.2 0.4
F1 A:LE9401 2.1 25.8 0.4
F3 A:LE9401 2.1 27.5 0.4
C3 A:LE9401 2.2 40.4 0.4
C3 A:LE9401 2.3 33.5 0.4
F3 A:LE9401 2.5 42.0 0.4
N2 A:LE9401 2.6 39.8 0.4
C1 A:LE9401 3.0 36.3 0.4
BR1 A:LE9401 3.2 39.9 0.4
CG A:PRO151 3.3 20.6 1.0
N2 A:LE9401 3.5 33.5 0.4
C1 A:LE9401 3.5 39.8 0.4
CB A:CYS220 3.7 21.8 0.8
CD A:PRO151 3.7 18.2 1.0
SG A:CYS220 3.8 27.5 0.8
N1 A:LE9401 3.9 39.5 0.4
C2 A:LE9401 4.3 35.7 0.4
C2 A:LE9401 4.3 39.9 0.4
CD1 A:LEU257 4.4 15.3 1.0
N1 A:LE9401 4.5 34.8 0.4
CG1 A:VAL147 4.5 17.1 1.0
BR1 A:LE9401 4.6 40.0 0.4
CB A:PRO151 4.8 18.4 1.0
CA A:CYS220 4.9 20.9 1.0
CG2 A:VAL147 4.9 17.4 1.0
CG2 A:THR155 5.0 14.7 1.0

Fluorine binding site 4 out of 9 in 8a92

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Fluorine binding site 4 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.9
occ:0.40
 F2 A:LE9401 0.0 42.9 0.4
F2 A:LE9401 1.0 32.2 0.4
C4 A:LE9401 1.3 29.8 0.4
F3 A:LE9401 1.3 27.5 0.4
C4 A:LE9401 1.3 41.6 0.4
F3 A:LE9401 2.1 42.0 0.4
F1 A:LE9401 2.1 41.2 0.4
C3 A:LE9401 2.3 33.5 0.4
C3 A:LE9401 2.3 40.4 0.4
F1 A:LE9401 2.3 25.8 0.4
N2 A:LE9401 2.8 39.8 0.4
C1 A:LE9401 2.9 36.3 0.4
BR1 A:LE9401 3.0 39.9 0.4
CB A:CYS220 3.0 21.8 0.8
SG A:CYS220 3.4 27.5 0.8
N2 A:LE9401 3.6 33.5 0.4
C1 A:LE9401 3.6 39.8 0.4
CA A:CYS220 4.0 20.9 1.0
N1 A:LE9401 4.1 39.5 0.4
CG A:PRO151 4.2 20.6 1.0
O A:GLU221 4.3 27.0 1.0
C2 A:LE9401 4.3 35.7 0.4
C A:CYS220 4.4 24.4 1.0
C2 A:LE9401 4.5 39.9 0.4
N1 A:LE9401 4.6 34.8 0.4
N A:GLU221 4.6 25.1 1.0
CD A:PRO151 4.6 18.2 1.0
CD1 A:LEU145 4.6 18.7 1.0
BR1 A:LE9401 4.7 40.0 0.4
OG1 A:THR230 4.7 24.2 1.0
CD1 A:LEU257 4.8 15.3 1.0
C A:GLU221 4.9 28.4 1.0

Fluorine binding site 5 out of 9 in 8a92

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Fluorine binding site 5 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.5
occ:0.40
 F3 A:LE9401 0.0 27.5 0.4
F3 A:LE9401 1.2 42.0 0.4
F2 A:LE9401 1.3 42.9 0.4
C4 A:LE9401 1.3 29.8 0.4
C4 A:LE9401 1.4 41.6 0.4
F2 A:LE9401 2.1 32.2 0.4
F1 A:LE9401 2.1 25.8 0.4
C3 A:LE9401 2.3 33.5 0.4
C3 A:LE9401 2.4 40.4 0.4
F1 A:LE9401 2.6 41.2 0.4
N2 A:LE9401 3.2 39.8 0.4
C1 A:LE9401 3.2 36.3 0.4
N2 A:LE9401 3.3 33.5 0.4
C1 A:LE9401 3.3 39.8 0.4
OG1 A:THR230 3.6 24.2 1.0
O A:GLU221 3.6 27.0 1.0
CB A:CYS220 3.6 21.8 0.8
BR1 A:LE9401 3.7 39.9 0.4
CB A:THR230 3.7 21.0 1.0
CD1 A:LEU145 3.9 18.7 1.0
SG A:CYS220 3.9 27.5 0.8
BR1 A:LE9401 4.0 40.0 0.4
CG2 A:THR230 4.2 21.2 1.0
CA A:CYS220 4.2 20.9 1.0
N1 A:LE9401 4.3 39.5 0.4
C2 A:LE9401 4.3 35.7 0.4
N A:GLU221 4.4 25.1 1.0
C2 A:LE9401 4.4 39.9 0.4
CB A:LEU145 4.4 15.5 1.0
N1 A:LE9401 4.4 34.8 0.4
C A:GLU221 4.5 28.4 1.0
C A:CYS220 4.6 24.4 1.0
O A:HOH653 4.7 34.4 1.0
CG A:LEU145 4.8 15.7 1.0

Fluorine binding site 6 out of 9 in 8a92

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Fluorine binding site 6 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:42.0
occ:0.40
 F3 A:LE9401 0.0 42.0 0.4
F3 A:LE9401 1.2 27.5 0.4
F1 A:LE9401 1.3 25.8 0.4
C4 A:LE9401 1.3 41.6 0.4
C4 A:LE9401 1.4 29.8 0.4
F2 A:LE9401 2.1 42.9 0.4
F1 A:LE9401 2.1 41.2 0.4
C3 A:LE9401 2.4 40.4 0.4
F2 A:LE9401 2.5 32.2 0.4
C3 A:LE9401 2.5 33.5 0.4
C1 A:LE9401 3.0 39.8 0.4
N2 A:LE9401 3.1 33.5 0.4
BR1 A:LE9401 3.1 40.0 0.4
CB A:LEU145 3.4 15.5 1.0
N2 A:LE9401 3.5 39.8 0.4
CD1 A:LEU145 3.6 18.7 1.0
CB A:THR230 3.6 21.0 1.0
OG1 A:THR230 3.7 24.2 1.0
C1 A:LE9401 3.7 36.3 0.4
CG A:LEU145 4.1 15.7 1.0
O A:LEU145 4.2 17.0 1.0
C2 A:LE9401 4.3 39.9 0.4
N1 A:LE9401 4.4 34.8 0.4
CG2 A:THR230 4.4 21.2 1.0
O A:GLU221 4.5 27.0 1.0
C A:LEU145 4.5 13.7 1.0
N1 A:LE9401 4.6 39.5 0.4
BR1 A:LE9401 4.6 39.9 0.4
CA A:LEU145 4.6 13.1 1.0
C2 A:LE9401 4.6 35.7 0.4
SG A:CYS220 4.7 27.5 0.8
CB A:CYS220 4.7 21.8 0.8
CA A:THR230 4.8 18.8 1.0
N A:THR230 4.8 20.0 1.0

Fluorine binding site 7 out of 9 in 8a92

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Fluorine binding site 7 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:52.1
occ:0.60
 F1 B:LE9403 0.0 52.1 0.6
C4 B:LE9403 1.3 51.0 0.6
F3 B:LE9403 2.1 52.4 0.6
F2 B:LE9403 2.1 50.1 0.6
OG1 B:THR230 2.3 21.9 0.5
C3 B:LE9403 2.4 50.1 0.6
C1 B:LE9403 3.0 49.8 0.6
BR1 B:LE9403 3.1 50.0 0.6
OG1 B:THR230 3.2 22.7 0.5
CB B:THR230 3.3 20.6 0.5
CB B:LEU145 3.4 16.4 1.0
N2 B:LE9403 3.5 49.7 0.6
CB B:THR230 3.5 20.9 0.5
CD1 B:LEU145 3.7 20.4 1.0
CG2 B:THR230 3.8 21.5 0.5
O B:GLU221 3.9 36.5 1.0
O B:LEU145 4.1 16.7 1.0
CG2 B:THR230 4.2 20.2 0.5
CG B:LEU145 4.2 16.5 1.0
C2 B:LE9403 4.3 49.9 0.6
O B:HOH679 4.4 45.1 1.0
CA B:THR230 4.5 18.3 0.5
N B:THR230 4.5 18.2 1.0
C B:LEU145 4.6 13.7 1.0
N1 B:LE9403 4.6 49.3 0.6
CA B:THR230 4.6 18.6 0.5
CA B:LEU145 4.6 14.2 1.0

Fluorine binding site 8 out of 9 in 8a92

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Fluorine binding site 8 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:50.1
occ:0.60
 F2 B:LE9403 0.0 50.1 0.6
C4 B:LE9403 1.3 51.0 0.6
F1 B:LE9403 2.1 52.1 0.6
F3 B:LE9403 2.1 52.4 0.6
C3 B:LE9403 2.3 50.1 0.6
N2 B:LE9403 3.2 49.7 0.6
C1 B:LE9403 3.3 49.8 0.6
BR1 B:LE9403 3.9 50.0 0.6
CG1 B:VAL147 4.0 16.2 1.0
SG B:CYS220 4.0 27.8 0.6
CB B:LEU145 4.1 16.4 1.0
CD1 B:LEU145 4.3 20.4 1.0
N1 B:LE9403 4.3 49.3 0.6
CD1 B:LEU257 4.4 16.4 1.0
C2 B:LE9403 4.4 49.9 0.6
OG1 B:THR230 4.4 21.9 0.5
CB B:CYS220 4.6 26.7 0.6
CG B:PRO151 4.7 19.8 1.0
CG2 B:VAL147 4.8 16.2 1.0
CG2 B:VAL157 4.8 17.2 1.0
CE1 B:PHE109 4.9 15.2 1.0
CG B:LEU145 4.9 16.5 1.0
CD B:PRO151 5.0 18.4 1.0
CD1 B:PHE109 5.0 15.2 1.0

Fluorine binding site 9 out of 9 in 8a92

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Fluorine binding site 9 out of 9 in the P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of P53-Y220C Core Domain in Complex with A Bromo-Trifluoro-Pyrazole-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:52.4
occ:0.60
 F3 B:LE9403 0.0 52.4 0.6
C4 B:LE9403 1.3 51.0 0.6
F1 B:LE9403 2.1 52.1 0.6
F2 B:LE9403 2.1 50.1 0.6
C3 B:LE9403 2.3 50.1 0.6
N2 B:LE9403 2.8 49.7 0.6
CB B:CYS220 3.1 26.7 0.6
SG B:CYS220 3.3 27.8 0.6
O B:GLU221 3.4 36.5 1.0
CA B:CYS220 3.6 26.9 1.0
C1 B:LE9403 3.6 49.8 0.6
N B:GLU221 3.8 34.1 1.0
OG1 B:THR230 4.0 21.9 0.5
O B:HOH679 4.0 45.1 1.0
C B:CYS220 4.0 33.4 1.0
N1 B:LE9403 4.1 49.3 0.6
O B:HOH571 4.1 40.0 1.0
C B:GLU221 4.2 37.8 1.0
OG1 B:THR230 4.4 22.7 0.5
C2 B:LE9403 4.5 49.9 0.6
CD1 B:LEU145 4.6 20.4 1.0
BR1 B:LE9403 4.7 50.0 0.6
CA B:GLU221 4.7 36.0 1.0
CB B:THR230 4.8 20.6 0.5
CG2 B:THR230 4.8 21.5 0.5
CG2 B:VAL157 4.9 17.2 1.0
N B:CYS220 4.9 22.1 1.0
CB B:THR230 5.0 20.9 0.5

Reference:

J.Stahlecker, T.Klett, M.Schwer, S.Jaag, M.Dammann, L.N.Ernst, M.B.Braun, M.O.Zimmermann, M.Kramer, M.Laemmerhofer, T.Stehle, M.Coles, F.M.Boeckler. Revisiting A Challenging P53 Binding Site: A Diversity-Optimized Heflib Reveals Diverse Binding Modes in T-P53C-Y220C Rsc Med Chem 2022.
ISSN: ESSN 2632-8682
DOI: 10.1039/D2MD00246A
Page generated: Fri Aug 2 16:30:20 2024

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