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

The structure of P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 Mm, PDB code: 8rba 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)	47.82 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.913, 70.705, 105.33, 90, 90, 90
R / Rfree (%)	15 / 18.3

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

Zinc

(Zn)

2 atoms

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

Fluorine binding site 1 out of 4 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 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 5 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:43.9 occ:1.00 F1 A:YLW401 0.0 43.9 1.0 C4 A:YLW401 1.4 39.8 1.0 C5 A:YLW401 2.4 35.5 1.0 C3 A:YLW401 2.4 38.1 1.0 SG A:CYS220 3.0 35.1 1.0 CB A:LEU145 3.2 18.6 1.0 CD1 A:LEU145 3.6 25.6 1.0 N1 A:YLW401 3.6 36.4 1.0 CG2 A:THR230 3.6 27.9 0.5 C2 A:YLW401 3.6 38.0 1.0 CG A:LEU145 4.0 20.6 1.0 O A:HOH553 4.0 29.6 1.0 C1 A:YLW401 4.1 37.1 1.0 CG1 A:VAL147 4.1 23.0 1.0 O A:LEU145 4.2 22.4 1.0 C A:LEU145 4.3 19.2 1.0 CA A:LEU145 4.3 16.9 1.0 CD1 A:LEU257 4.4 19.6 1.0 CE1 A:PHE109 4.4 19.8 1.0 CD1 A:PHE109 4.6 19.4 1.0 CB A:CYS220 4.6 28.7 1.0 OG1 A:THR230 4.7 25.6 0.5 CB A:THR230 4.7 25.4 0.5 C6 A:YLW401 4.9 38.0 1.0 N A:TRP146 4.9 19.2 1.0 CG2 A:VAL147 5.0 23.1 1.0

Fluorine binding site 2 out of 4 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 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 5 Mm within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:37.8 occ:1.00 F2 A:YLW401 0.0 37.8 1.0 C1 A:YLW401 1.3 37.1 1.0 N1 A:YLW401 2.3 36.4 1.0 C2 A:YLW401 2.4 38.0 1.0 C6 A:YLW401 2.8 38.0 1.0 N A:PRO222 3.3 33.5 1.0 C A:GLU221 3.4 31.7 1.0 CD A:PRO222 3.5 34.5 1.0 N2 A:YLW401 3.5 40.7 1.0 C5 A:YLW401 3.5 35.5 1.0 O A:HOH625 3.5 57.0 1.0 O A:HOH547 3.6 54.9 1.0 CG A:PRO222 3.6 37.4 1.0 C3 A:YLW401 3.6 38.1 1.0 O A:GLU221 3.7 30.8 1.0 CA A:PRO222 3.7 35.0 1.0 O A:CYS220 3.7 32.6 1.0 CG A:PRO151 3.8 24.8 1.0 CD A:PRO151 3.9 23.4 1.0 CA A:GLU221 4.0 33.0 1.0 C4 A:YLW401 4.0 39.8 1.0 C A:CYS220 4.1 29.3 1.0 CG2 A:THR150 4.1 30.9 1.0 CB A:PRO222 4.2 35.5 1.0 N A:GLU221 4.2 30.8 1.0 O A:PRO151 4.4 24.8 1.0 N A:PRO151 4.7 22.8 1.0 CB A:CYS220 4.7 28.7 1.0 SG A:CYS220 4.9 35.1 1.0

Fluorine binding site 3 out of 4 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 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 5 Mm within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:42.5 occ:1.00 F1 B:YLW401 0.0 42.5 1.0 C4 B:YLW401 1.4 41.3 1.0 C5 B:YLW401 2.4 38.4 1.0 C3 B:YLW401 2.4 40.5 1.0 SG B:CYS220 2.8 36.7 1.0 CB B:LEU145 3.3 19.9 1.0 N1 B:YLW401 3.6 40.9 1.0 C2 B:YLW401 3.6 40.5 1.0 CG2 B:THR230 3.7 27.0 0.5 CD1 B:LEU145 3.8 24.4 1.0 O B:HOH552 4.0 25.3 1.0 C1 B:YLW401 4.1 39.9 1.0 CG B:LEU145 4.2 20.1 1.0 CG1 B:VAL147 4.2 18.9 1.0 O B:LEU145 4.3 22.7 1.0 C B:LEU145 4.4 18.9 1.0 CB B:CYS220 4.5 27.0 1.0 CA B:LEU145 4.5 17.0 1.0 OG1 B:THR230 4.6 29.8 0.5 CE1 B:PHE109 4.6 18.6 1.0 CD1 B:LEU257 4.7 19.1 1.0 CB B:THR230 4.7 27.5 0.5 O B:GLU221 4.7 29.3 1.0 CD1 B:PHE109 4.7 18.7 1.0 CG2 B:VAL157 4.8 19.2 0.5 C6 B:YLW401 4.9 42.0 1.0 CG2 B:VAL147 4.9 20.1 1.0

Fluorine binding site 4 out of 4 in the P53-Y220C Core Domain Covalently Bound to 2,5,6-Trifluoropyridine-3- Carbonitrile Soaked at 5 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 5 Mm within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:39.4 occ:1.00 F2 B:YLW401 0.0 39.4 1.0 C1 B:YLW401 1.3 39.9 1.0 N1 B:YLW401 2.3 40.9 1.0 C2 B:YLW401 2.4 40.5 1.0 C6 B:YLW401 2.8 42.0 1.0 O B:HOH626 3.1 49.1 1.0 N B:PRO222 3.4 32.4 1.0 C5 B:YLW401 3.5 38.4 1.0 CG B:PRO222 3.5 34.5 1.0 N2 B:YLW401 3.6 45.0 1.0 CD B:PRO151 3.6 21.2 1.0 C B:GLU221 3.6 30.4 1.0 CD B:PRO222 3.6 34.5 1.0 C3 B:YLW401 3.6 40.5 1.0 O B:HOH564 3.7 57.5 1.0 CA B:PRO222 3.7 32.0 1.0 CG B:PRO151 3.7 22.1 1.0 CG2 B:THR150 3.8 26.0 1.0 O B:CYS220 4.0 33.4 1.0 O B:GLU221 4.0 29.3 1.0 CB B:PRO222 4.0 33.8 1.0 C4 B:YLW401 4.0 41.3 1.0 CA B:GLU221 4.2 32.3 1.0 C B:CYS220 4.3 29.8 1.0 O B:PRO151 4.3 22.7 1.0 N B:GLU221 4.4 28.9 1.0 N B:PRO151 4.5 20.8 1.0 CB B:CYS220 4.8 27.0 1.0 CB B:THR150 5.0 27.2 1.0 SG B:CYS220 5.0 36.7 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