Fluorine in PDB 6si3: P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301

The structure of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301, PDB code: 6si3 was solved by A.C.Joerger, M.R.Bauer, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.982, 71.298, 105.417, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.6

The structure of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 (pdb code 6si3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301, PDB code: 6si3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:18.5 occ:1.00 F2 A:LEB402 0.0 18.5 1.0 C7 A:LEB402 1.3 18.0 1.0 F A:LEB402 2.1 18.4 1.0 F1 A:LEB402 2.1 20.0 1.0 C6 A:LEB402 2.3 17.9 1.0 OG A:SER220 3.1 25.1 1.0 O A:HOH679 3.4 31.6 1.0 CD1 A:LEU145 3.5 18.2 1.0 CB A:LEU145 3.5 14.2 1.0 N1 A:LEB402 3.6 18.5 1.0 CG2 A:VAL157 3.8 15.3 1.0 CD1 A:LEU257 3.8 14.6 1.0 CE1 A:PHE109 4.0 14.7 1.0 CG A:LEU145 4.0 15.3 1.0 CB A:SER220 4.4 21.4 1.0 CD1 A:PHE109 4.5 13.9 1.0 C8 A:LEB402 4.5 24.0 1.0 C5 A:LEB402 4.5 16.4 1.0 C13 A:LEB402 4.6 34.6 1.0 CD2 A:LEU145 4.7 15.5 1.0 CA A:LEU145 4.8 12.2 1.0 C4 A:LEB402 4.8 16.2 1.0 CG1 A:VAL147 4.9 14.5 1.0 C A:LEU145 4.9 12.1 1.0

Fluorine binding site 2 out of 6 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:20.0 occ:1.00 F1 A:LEB402 0.0 20.0 1.0 C7 A:LEB402 1.3 18.0 1.0 F A:LEB402 2.1 18.4 1.0 F2 A:LEB402 2.1 18.5 1.0 C6 A:LEB402 2.4 17.9 1.0 N1 A:LEB402 2.8 18.5 1.0 OG A:SER220 3.0 25.1 1.0 C8 A:LEB402 3.2 24.0 1.0 C13 A:LEB402 3.3 34.6 1.0 CG A:PRO151 3.7 18.4 1.0 CD1 A:LEU257 3.7 14.6 1.0 C5 A:LEB402 3.7 16.4 1.0 CG1 A:VAL147 3.8 14.5 1.0 CD A:PRO151 4.2 16.4 1.0 C9 A:LEB402 4.2 23.2 1.0 CB A:SER220 4.3 21.4 1.0 C4 A:LEB402 4.4 16.2 1.0 CG2 A:VAL147 4.4 15.6 1.0 C12 A:LEB402 4.5 46.3 1.0 CD2 A:LEU257 4.5 15.4 1.0 C14 A:LEB402 4.5 18.4 1.0 O A:HOH679 4.7 31.6 1.0 CB A:VAL147 4.8 14.0 1.0 CG A:LEU257 4.8 13.6 1.0 CB A:PRO151 4.9 17.5 1.0 CD1 A:PHE109 4.9 13.9 1.0

Fluorine binding site 3 out of 6 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:18.4 occ:1.00 F A:LEB402 0.0 18.4 1.0 C7 A:LEB402 1.3 18.0 1.0 F2 A:LEB402 2.1 18.5 1.0 F1 A:LEB402 2.1 20.0 1.0 C6 A:LEB402 2.4 17.9 1.0 N1 A:LEB402 2.9 18.5 1.0 C4 A:LEB402 3.3 16.2 1.0 CG1 A:VAL147 3.3 14.5 1.0 C5 A:LEB402 3.3 16.4 1.0 CB A:LEU145 3.7 14.2 1.0 O A:LEU145 3.9 13.4 1.0 C A:LEU145 3.9 12.1 1.0 CG2 A:VAL147 3.9 15.6 1.0 C8 A:LEB402 4.0 24.0 1.0 CB A:VAL147 4.1 14.0 1.0 C A:TRP146 4.2 13.2 1.0 N A:TRP146 4.2 12.0 1.0 CD1 A:PHE109 4.2 13.9 1.0 N A:VAL147 4.3 13.3 1.0 CE1 A:PHE109 4.3 14.7 1.0 O A:TRP146 4.3 14.1 1.0 CA A:LEU145 4.4 12.2 1.0 C3 A:LEB402 4.4 16.6 1.0 C14 A:LEB402 4.5 18.4 1.0 CA A:TRP146 4.6 12.5 1.0 OG A:SER220 4.6 25.1 1.0 C13 A:LEB402 4.8 34.6 1.0 CA A:VAL147 4.8 13.4 1.0 CG A:LEU145 4.9 15.3 1.0 CD1 A:LEU145 4.9 18.2 1.0 C9 A:LEB402 4.9 23.2 1.0 CD1 A:LEU257 5.0 14.6 1.0

Fluorine binding site 4 out of 6 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:17.9 occ:1.00 F2 B:LEB402 0.0 17.9 1.0 C7 B:LEB402 1.3 18.2 1.0 F B:LEB402 2.1 18.6 1.0 F1 B:LEB402 2.1 19.9 1.0 C6 B:LEB402 2.3 17.7 1.0 OG B:SER220 3.0 22.5 1.0 O B:HOH633 3.4 30.3 1.0 CB B:LEU145 3.4 15.1 1.0 CD1 B:LEU145 3.4 20.2 1.0 N1 B:LEB402 3.6 19.4 1.0 CD1 B:LEU257 3.7 14.0 1.0 CG2 B:VAL157 3.8 16.8 1.0 CG B:LEU145 4.0 17.3 1.0 CE1 B:PHE109 4.1 15.1 1.0 CB B:SER220 4.3 19.8 1.0 C8 B:LEB402 4.5 24.2 1.0 CD1 B:PHE109 4.5 15.1 1.0 C5 B:LEB402 4.5 17.7 1.0 C13 B:LEB402 4.7 34.5 1.0 CD2 B:LEU145 4.7 17.3 1.0 CA B:LEU145 4.7 13.6 1.0 C4 B:LEB402 4.8 17.7 1.0 C B:LEU145 4.9 13.5 1.0 CG1 B:VAL147 5.0 17.5 1.0

Fluorine binding site 5 out of 6 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:19.9 occ:1.00 F1 B:LEB402 0.0 19.9 1.0 C7 B:LEB402 1.3 18.2 1.0 F B:LEB402 2.1 18.6 1.0 F2 B:LEB402 2.1 17.9 1.0 C6 B:LEB402 2.4 17.7 1.0 N1 B:LEB402 2.8 19.4 1.0 OG B:SER220 3.1 22.5 1.0 C8 B:LEB402 3.2 24.2 1.0 C13 B:LEB402 3.4 34.5 1.0 CG B:PRO151 3.6 18.7 1.0 CD1 B:LEU257 3.7 14.0 1.0 C5 B:LEB402 3.7 17.7 1.0 CG1 B:VAL147 3.9 17.5 1.0 CD B:PRO151 4.1 17.6 1.0 C9 B:LEB402 4.3 23.4 1.0 CB B:SER220 4.3 19.8 1.0 C4 B:LEB402 4.4 17.7 1.0 CG2 B:VAL147 4.5 18.9 1.0 C12 B:LEB402 4.5 45.7 1.0 CD2 B:LEU257 4.5 15.4 1.0 C14 B:LEB402 4.5 18.7 1.0 CG B:LEU257 4.7 13.9 1.0 O B:HOH633 4.8 30.3 1.0 CB B:PRO151 4.8 18.1 1.0 CB B:VAL147 4.8 16.1 1.0 CD1 B:PHE109 5.0 15.1 1.0

Fluorine binding site 6 out of 6 in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9301 within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:18.6 occ:1.00 F B:LEB402 0.0 18.6 1.0 C7 B:LEB402 1.3 18.2 1.0 F2 B:LEB402 2.1 17.9 1.0 F1 B:LEB402 2.1 19.9 1.0 C6 B:LEB402 2.4 17.7 1.0 N1 B:LEB402 3.0 19.4 1.0 C4 B:LEB402 3.3 17.7 1.0 C5 B:LEB402 3.3 17.7 1.0 CG1 B:VAL147 3.3 17.5 1.0 CB B:LEU145 3.6 15.1 1.0 O B:LEU145 3.9 14.7 1.0 CG2 B:VAL147 3.9 18.9 1.0 C B:LEU145 3.9 13.5 1.0 C8 B:LEB402 4.1 24.2 1.0 CB B:VAL147 4.1 16.1 1.0 C B:TRP146 4.2 14.4 1.0 N B:TRP146 4.2 13.1 1.0 CD1 B:PHE109 4.3 15.1 1.0 N B:VAL147 4.3 14.7 1.0 O B:TRP146 4.3 14.8 1.0 CE1 B:PHE109 4.4 15.1 1.0 CA B:LEU145 4.4 13.6 1.0 C3 B:LEB402 4.4 18.0 1.0 C14 B:LEB402 4.5 18.7 1.0 OG B:SER220 4.6 22.5 1.0 CA B:TRP146 4.6 13.9 1.0 C13 B:LEB402 4.8 34.5 1.0 CA B:VAL147 4.8 15.3 1.0 CG B:LEU145 4.8 17.3 1.0 CD1 B:LEU145 4.8 20.2 1.0 CD1 B:LEU257 4.8 14.0 1.0 C9 B:LEB402 4.9 23.4 1.0

M.R.Bauer, A.Kramer, G.Settanni, R.N.Jones, X.Ni, R.Khan Tareque, A.R.Fersht, J.Spencer, A.C.Joerger. Targeting Cavity-Creating P53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 31990523
DOI: 10.1021/ACSCHEMBIO.9B00748