Fluorine in PDB 8rbb: P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm

The structure of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm, PDB code: 8rbb was solved by J.Stahlecker, T.Klett, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.97 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.083, 70.989, 105.94, 90, 90, 90
R / Rfree (%)	16.4 / 20.7

The structure of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm (pdb code 8rbb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm, PDB code: 8rbb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:67.8 occ:1.00 F1 A:YLW401 0.0 67.8 1.0 C4 A:YLW401 1.4 64.4 1.0 C5 A:YLW401 2.3 61.8 1.0 C3 A:YLW401 2.4 64.3 1.0 SG A:CYS124 2.8 55.7 1.0 N1 A:YLW401 3.6 63.9 1.0 C2 A:YLW401 3.6 65.4 1.0 CD A:PRO142 3.7 31.8 1.0 CG A:PRO142 3.9 36.0 1.0 C1 A:YLW401 4.1 63.9 1.0 O A:HOH552 4.3 60.7 1.0 O A:THR140 4.4 35.1 1.0 CB A:CYS124 4.5 47.1 1.0 O A:CYS124 4.5 37.1 1.0 OG A:SER116 4.8 75.4 1.0 C6 A:YLW401 4.8 68.4 1.0 OG1 A:THR123 4.9 40.6 1.0

Fluorine binding site 2 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:62.8 occ:1.00 F2 A:YLW401 0.0 62.8 1.0 C1 A:YLW401 1.3 63.9 1.0 N1 A:YLW401 2.3 63.9 1.0 C2 A:YLW401 2.4 65.4 1.0 C6 A:YLW401 2.8 68.4 1.0 O A:HOH569 3.2 56.8 1.0 N A:TYR126 3.4 30.4 1.0 CB A:TYR126 3.5 28.9 1.0 C5 A:YLW401 3.5 61.8 1.0 N2 A:YLW401 3.6 70.9 1.0 C3 A:YLW401 3.7 64.3 1.0 CD1 A:LEU133 3.8 35.7 1.0 C A:THR125 3.9 33.1 1.0 CA A:THR125 3.9 34.7 1.0 CD2 A:PHE113 3.9 37.4 1.0 CA A:TYR126 4.0 28.8 1.0 C4 A:YLW401 4.1 64.4 1.0 N A:THR125 4.2 34.7 1.0 O A:LEU114 4.3 62.6 1.0 O A:CYS124 4.4 37.1 1.0 C A:CYS124 4.4 38.0 1.0 CB A:PHE113 4.5 34.9 1.0 CG A:PHE113 4.6 34.1 1.0 O A:THR125 4.6 32.8 1.0 OG A:SER116 4.7 75.4 1.0 O A:HOH517 4.8 51.7 1.0 CE2 A:PHE113 4.8 37.8 1.0 CG A:TYR126 4.8 29.6 1.0 O A:PRO142 4.9 33.8 1.0 CB A:CYS124 4.9 47.1 1.0

Fluorine binding site 3 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:66.5 occ:1.00 F1 A:YLW402 0.0 66.5 1.0 C4 A:YLW402 1.4 63.1 1.0 C3 A:YLW402 2.4 61.4 1.0 C5 A:YLW402 2.4 60.5 1.0 SG A:CYS220 3.1 60.7 1.0 CB A:LEU145 3.5 33.9 1.0 N1 A:YLW402 3.6 59.1 1.0 C2 A:YLW402 3.6 62.6 1.0 O A:HOH596 3.8 55.4 1.0 CD1 A:LEU145 3.9 39.5 1.0 C1 A:YLW402 4.1 59.7 1.0 OG1 A:THR230 4.2 47.3 1.0 CG1 A:VAL147 4.2 37.8 1.0 CB A:THR230 4.3 45.3 1.0 CG A:LEU145 4.4 37.2 1.0 C A:LEU145 4.4 33.0 1.0 O A:LEU145 4.4 36.1 1.0 CE1 A:PHE109 4.6 28.0 1.0 CA A:LEU145 4.6 32.1 1.0 CG2 A:THR230 4.7 45.5 1.0 N A:TRP146 4.8 32.4 1.0 O A:GLU221 4.8 57.1 1.0 CD1 A:PHE109 4.8 29.3 1.0 CG2 A:VAL147 4.8 38.8 1.0 CD1 A:LEU257 4.8 26.7 1.0 CB A:CYS220 4.8 51.0 1.0 C6 A:YLW402 4.8 63.3 1.0 C A:TRP146 4.9 34.7 1.0

Fluorine binding site 4 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:59.0 occ:1.00 F2 A:YLW402 0.0 59.0 1.0 C1 A:YLW402 1.3 59.7 1.0 N1 A:YLW402 2.3 59.1 1.0 C2 A:YLW402 2.4 62.6 1.0 O A:HOH506 2.7 67.7 1.0 C6 A:YLW402 2.8 63.3 1.0 N A:PRO222 3.3 61.8 1.0 C A:GLU221 3.5 59.4 1.0 C5 A:YLW402 3.5 60.5 1.0 CD A:PRO151 3.5 32.1 1.0 N2 A:YLW402 3.5 64.0 1.0 O A:HOH604 3.5 59.2 1.0 CD A:PRO222 3.6 63.4 1.0 CA A:PRO222 3.6 64.6 1.0 C3 A:YLW402 3.6 61.4 1.0 CG A:PRO222 3.7 65.3 1.0 O A:GLU221 3.7 57.1 1.0 CG2 A:THR150 3.8 44.6 1.0 CG A:PRO151 3.8 34.5 1.0 C4 A:YLW402 4.0 63.1 1.0 CB A:PRO222 4.1 64.9 1.0 CA A:GLU221 4.2 58.3 1.0 O A:CYS220 4.3 56.8 1.0 N A:GLU221 4.4 54.8 1.0 C A:CYS220 4.4 52.4 1.0 N A:PRO151 4.4 34.3 1.0 O A:PRO151 4.5 33.2 1.0 SG A:CYS220 4.8 60.7 1.0 CB A:THR150 4.8 43.0 1.0 CB A:CYS220 4.9 51.0 1.0 CA A:THR150 4.9 40.6 1.0 C A:PRO222 5.0 63.8 1.0

Fluorine binding site 5 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:58.8 occ:1.00 F1 A:YLW403 0.0 58.8 1.0 C4 A:YLW403 1.3 58.6 1.0 C5 A:YLW403 2.3 56.6 1.0 C3 A:YLW403 2.4 59.5 1.0 SG A:CYS229 2.8 57.3 1.0 N1 A:YLW403 3.6 54.9 1.0 C2 A:YLW403 3.6 58.3 1.0 C1 A:YLW403 4.0 53.8 1.0 CB A:ASP228 4.2 67.0 1.0 CE3 A:TRP146 4.3 55.1 1.0 CZ3 A:TRP146 4.5 57.3 1.0 CB A:CYS229 4.6 52.3 1.0 O A:ASP228 4.7 64.5 1.0 C A:ASP228 4.8 64.0 1.0 C6 A:YLW403 4.8 55.0 1.0 O A:HOH612 4.9 63.1 1.0

Fluorine binding site 6 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:52.7 occ:1.00 F2 A:YLW403 0.0 52.7 1.0 C1 A:YLW403 1.3 53.8 1.0 N1 A:YLW403 2.3 54.9 1.0 C2 A:YLW403 2.4 58.3 1.0 C6 A:YLW403 2.8 55.0 1.0 CB A:TRP146 3.3 37.2 1.0 N A:TRP146 3.4 32.4 1.0 N2 A:YLW403 3.5 54.8 1.0 C5 A:YLW403 3.5 56.6 1.0 C A:LEU145 3.5 33.0 1.0 N A:GLY112 3.5 32.0 1.0 O A:GLN144 3.5 30.9 1.0 C A:GLN144 3.6 30.4 1.0 CB A:GLN144 3.6 31.7 1.0 C3 A:YLW403 3.6 59.5 1.0 N A:LEU145 3.8 30.5 1.0 CA A:GLY112 3.8 33.6 1.0 CA A:TRP146 3.9 33.5 1.0 C A:LEU111 3.9 30.7 1.0 O A:LEU145 3.9 36.1 1.0 CA A:LEU145 3.9 32.1 1.0 C4 A:YLW403 4.0 58.6 1.0 O A:ARG110 4.1 32.0 1.0 O A:HOH612 4.1 63.1 1.0 CA A:GLN144 4.3 28.3 1.0 O A:LEU111 4.3 34.5 1.0 CA A:LEU111 4.4 29.6 1.0 CG A:TRP146 4.7 46.9 1.0 C A:GLY112 4.7 34.3 1.0 C A:ARG110 4.8 30.0 1.0 CG A:GLN144 4.8 39.8 1.0 O A:GLY112 4.9 32.1 1.0 CB A:CYS229 4.9 52.3 1.0 N A:LEU111 5.0 29.8 1.0 SG A:CYS229 5.0 57.3 1.0

Fluorine binding site 7 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:78.0 occ:1.00 F1 A:YLW404 0.0 78.0 1.0 C4 A:YLW404 1.4 74.9 1.0 C3 A:YLW404 2.4 76.0 1.0 C5 A:YLW404 2.4 69.8 1.0 SG A:CYS277 2.9 60.7 1.0 N1 A:YLW404 3.6 73.9 1.0 C2 A:YLW404 3.6 77.1 1.0 C1 A:YLW404 4.1 77.3 1.0 CB A:ALA276 4.5 44.7 1.0 O A:ALA276 4.6 46.3 1.0 CB A:CYS277 4.6 52.8 1.0 C A:ALA276 4.8 44.6 1.0 C6 A:YLW404 4.9 76.9 1.0

Fluorine binding site 8 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:79.7 occ:1.00 F2 A:YLW404 0.0 79.7 1.0 C1 A:YLW404 1.3 77.3 1.0 N1 A:YLW404 2.3 73.9 1.0 C2 A:YLW404 2.4 77.1 1.0 C6 A:YLW404 2.8 76.9 1.0 N A:SER121 3.5 69.9 1.0 C5 A:YLW404 3.5 69.8 1.0 C3 A:YLW404 3.6 76.0 1.0 C4 A:YLW404 4.1 74.9 1.0 CA A:SER121 4.7 70.2 1.0 CB A:CYS277 4.8 52.8 1.0 CA A:CYS277 5.0 45.2 1.0 SG A:CYS277 5.0 60.7 1.0

Fluorine binding site 9 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


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 Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F405 b:75.0 occ:1.00 F1 A:YLW405 0.0 75.0 1.0 C4 A:YLW405 1.4 73.2 1.0 C5 A:YLW405 2.4 66.3 1.0 C3 A:YLW405 2.4 76.1 1.0 NE2 A:HIS178 2.9 58.0 1.0 SG A:CYS182 3.1 55.8 1.0 O A:HOH509 3.2 58.3 1.0 CE1 A:HIS178 3.3 57.2 1.0 CD2 A:HIS179 3.4 35.4 1.0 NE2 A:HIS179 3.6 36.7 1.0 N1 A:YLW405 3.6 70.7 1.0 C2 A:YLW405 3.6 77.8 1.0 CD2 A:HIS178 3.8 56.5 1.0 C1 A:YLW405 4.1 75.8 1.0 ND1 A:HIS178 4.3 54.4 1.0 CG A:HIS179 4.5 32.8 1.0 CG A:HIS178 4.5 50.7 1.0 O A:HOH558 4.6 60.1 1.0 CB A:CYS182 4.8 51.8 1.0 CE1 A:HIS179 4.8 36.5 1.0 C6 A:YLW405 4.9 81.6 1.0

Fluorine binding site 10 out of 18 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 40 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F405 b:77.2 occ:1.00 F2 A:YLW405 0.0 77.2 1.0 C1 A:YLW405 1.3 75.8 1.0 N1 A:YLW405 2.3 70.7 1.0 C2 A:YLW405 2.4 77.8 1.0 C6 A:YLW405 2.8 81.6 1.0 C5 A:YLW405 3.5 66.3 1.0 N2 A:YLW405 3.5 84.3 1.0 C3 A:YLW405 3.6 76.1 1.0 C4 A:YLW405 4.0 73.2 1.0 N A:SER183 4.6 53.9 1.0 O A:SER183 4.6 61.1 1.0 CB A:CYS182 4.7 51.8 1.0 SG A:CYS182 4.9 55.8 1.0 C A:SER183 4.9 58.9 1.0

T.Klett, J.Stahlecker, S.Jaag, B.Masberg, C.Knappe, M.Lammerhofer, M.Coles, T.Stehle, F.M.Boeckler. Covalent Fragments Acting As Tyrosine Mimics For Mutant P53-Y220C Rescue By Nucleophilic Aromatic Substitution Acs Pharmacol Transl Sci 2024.
ISSN: ESSN 2575-910
DOI: 10.1021/ACSPTSCI.4C00414