Fluorine in PDB 5g4n: Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4n was solved by A.C.Joerger, M.Bauer, R.N.Jones, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.47 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.046, 71.139, 105.168, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.8

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 (pdb code 5g4n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4n:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1294 b:25.9 occ:0.59 F1 A:O831294 0.0 25.9 0.6 C14 A:O831294 1.4 26.1 0.6 F2 A:O831294 2.2 26.4 0.6 C13 A:O831294 2.3 27.2 0.6 O A:HOH2083 2.8 21.9 0.4 O A:HOH2187 2.8 26.7 0.4 N1 A:O831294 3.0 28.3 0.6 C9 A:O831294 3.2 29.2 0.6 CG1 A:VAL147 3.2 15.8 1.0 C4 A:O831294 3.3 28.6 0.6 C A:LEU145 3.4 12.2 1.0 O A:LEU145 3.4 13.6 1.0 C A:TRP146 3.5 13.3 1.0 CB A:LEU145 3.5 13.3 1.0 N A:TRP146 3.5 11.8 1.0 CG2 A:VAL147 3.6 15.7 1.0 N A:VAL147 3.6 14.1 1.0 CA A:TRP146 3.8 12.6 1.0 O A:TRP146 3.8 13.7 1.0 CB A:VAL147 3.8 14.5 1.0 CA A:LEU145 4.0 11.8 1.0 C1 A:O831294 4.1 30.2 0.6 CA A:VAL147 4.3 13.9 1.0 C10 A:O831294 4.3 29.9 0.6 CG2 A:THR230 4.3 14.5 0.3 O A:HOH2084 4.4 19.4 0.4 C3 A:O831294 4.5 29.7 0.6 CD1 A:PHE109 4.6 13.0 1.0 O A:HOH2229 4.6 23.8 0.4 CE1 A:PHE109 4.7 13.8 1.0 CG A:LEU145 4.8 14.4 1.0 SG A:CYS220 4.8 25.1 1.0 C5 A:O831294 4.9 31.1 0.6 C2 A:O831294 4.9 30.6 0.6 CD1 A:LEU145 4.9 17.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1294 b:26.4 occ:0.59 F2 A:O831294 0.0 26.4 0.6 C14 A:O831294 1.4 26.1 0.6 F1 A:O831294 2.2 25.9 0.6 C13 A:O831294 2.4 27.2 0.6 O A:HOH2187 2.8 26.7 0.4 SG A:CYS220 3.2 25.1 1.0 CB A:LEU145 3.3 13.3 1.0 CD1 A:LEU145 3.5 17.6 1.0 N1 A:O831294 3.6 28.3 0.6 CG2 A:THR230 3.8 14.5 0.3 CG A:LEU145 4.0 14.4 1.0 O A:HOH2083 4.1 21.9 0.4 CE1 A:PHE109 4.4 13.8 1.0 C1 A:O831294 4.4 30.2 0.6 CD1 A:LEU257 4.5 13.6 1.0 CG2 A:VAL157 4.5 16.1 1.0 CG1 A:VAL147 4.5 15.8 1.0 CA A:LEU145 4.5 11.8 1.0 C A:LEU145 4.5 12.2 1.0 C4 A:O831294 4.5 28.6 0.6 C5 A:O831294 4.5 31.1 0.6 CB A:CYS220 4.6 21.1 1.0 O A:LEU145 4.6 13.6 1.0 CD1 A:PHE109 4.7 13.0 1.0 O A:HOH2229 4.7 23.8 0.4 C9 A:O831294 4.8 29.2 0.6 CD2 A:LEU145 4.9 14.9 1.0 O A:GLU221 4.9 23.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1293 b:29.9 occ:0.53 F1 B:O831293 0.0 29.9 0.5 F2 B:O831293 0.1 29.8 0.5 C14 B:O831293 1.3 29.3 0.5 C14 B:O831293 1.4 29.2 0.5 F1 B:O831293 2.2 28.4 0.5 F2 B:O831293 2.2 28.6 0.5 C13 B:O831293 2.4 29.6 0.5 C13 B:O831293 2.4 29.7 0.5 N1 B:O831293 3.0 30.1 1.0 C9 B:O831293 3.2 30.9 1.0 CG1 B:VAL147 3.2 16.6 1.0 C4 B:O831293 3.2 30.3 1.0 C B:LEU145 3.5 13.4 1.0 O B:LEU145 3.5 15.4 1.0 CG2 B:VAL147 3.5 16.9 1.0 C B:TRP146 3.5 14.5 1.0 N B:VAL147 3.6 14.6 1.0 CB B:LEU145 3.6 14.1 1.0 N B:TRP146 3.6 12.8 1.0 CB B:VAL147 3.8 15.7 1.0 O B:TRP146 3.8 15.2 1.0 CA B:TRP146 3.8 13.5 1.0 C1 B:O831293 4.1 31.2 1.0 CA B:LEU145 4.1 12.5 1.0 CA B:VAL147 4.2 15.3 1.0 C10 B:O831293 4.3 30.6 1.0 C3 B:O831293 4.4 31.2 1.0 CD1 B:PHE109 4.5 13.6 1.0 SG B:CYS220 4.6 24.0 0.4 CE1 B:PHE109 4.6 14.6 1.0 C5 B:O831293 4.8 32.4 1.0 C2 B:O831293 4.8 31.4 1.0 SG B:CYS220 4.8 21.7 0.6 CG B:LEU145 4.9 14.9 1.0 CD1 B:LEU145 5.0 17.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1293 b:28.4 occ:0.47 F1 B:O831293 0.0 28.4 0.5 C14 B:O831293 1.3 29.2 0.5 C14 B:O831293 1.4 29.3 0.5 F2 B:O831293 2.1 28.6 0.5 F1 B:O831293 2.2 29.9 0.5 F2 B:O831293 2.2 29.8 0.5 C13 B:O831293 2.4 29.6 0.5 C13 B:O831293 2.4 29.7 0.5 N1 B:O831293 2.8 30.1 1.0 SG B:CYS220 3.1 21.7 0.6 C1 B:O831293 3.2 31.2 1.0 SG B:CYS220 3.3 24.0 0.4 C5 B:O831293 3.4 32.4 1.0 CG1 B:VAL147 3.5 16.6 1.0 CG B:PRO151 3.6 20.7 1.0 CG2 B:VAL147 3.6 16.9 1.0 C4 B:O831293 3.7 30.3 1.0 CD B:PRO151 3.9 19.7 1.0 C2 B:O831293 4.2 31.4 1.0 CB B:VAL147 4.2 15.7 1.0 C9 B:O831293 4.4 30.9 1.0 C3 B:O831293 4.4 31.2 1.0 CD1 B:LEU257 4.5 15.0 1.0 C6 B:O831293 4.5 33.1 1.0 CB B:CYS220 4.8 22.5 0.4 CB B:CYS220 4.8 20.4 0.6 CB B:PRO151 4.9 19.0 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1293 b:28.6 occ:0.53 F2 B:O831293 0.0 28.6 0.5 C14 B:O831293 1.3 29.3 0.5 C14 B:O831293 1.4 29.2 0.5 F1 B:O831293 2.1 28.4 0.5 F1 B:O831293 2.2 29.9 0.5 F2 B:O831293 2.2 29.8 0.5 C13 B:O831293 2.4 29.6 0.5 C13 B:O831293 2.4 29.7 0.5 SG B:CYS220 2.6 24.0 0.4 CB B:LEU145 3.1 14.1 1.0 SG B:CYS220 3.2 21.7 0.6 CD1 B:LEU145 3.4 17.1 1.0 N1 B:O831293 3.6 30.1 1.0 CG B:LEU145 3.9 14.9 1.0 CE1 B:PHE109 4.3 14.6 1.0 CD1 B:LEU257 4.3 15.0 1.0 CA B:LEU145 4.4 12.5 1.0 CB B:CYS220 4.4 22.5 0.4 C B:LEU145 4.4 13.4 1.0 C1 B:O831293 4.4 31.2 1.0 O B:LEU145 4.5 15.4 1.0 CG2 B:VAL157 4.5 14.9 0.7 C4 B:O831293 4.5 30.3 1.0 CD1 B:PHE109 4.6 13.6 1.0 C5 B:O831293 4.6 32.4 1.0 CG1 B:VAL147 4.6 16.6 1.0 CB B:CYS220 4.7 20.4 0.6 CD2 B:LEU145 4.8 14.9 1.0 C9 B:O831293 4.8 30.9 1.0 CB B:THR230 4.8 17.6 1.0 N B:TRP146 4.9 12.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Difluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1293 b:29.8 occ:0.47 F2 B:O831293 0.0 29.8 0.5 F1 B:O831293 0.1 29.9 0.5 C14 B:O831293 1.4 29.3 0.5 C14 B:O831293 1.4 29.2 0.5 F1 B:O831293 2.2 28.4 0.5 F2 B:O831293 2.2 28.6 0.5 C13 B:O831293 2.3 29.6 0.5 C13 B:O831293 2.3 29.7 0.5 N1 B:O831293 2.9 30.1 1.0 C9 B:O831293 3.1 30.9 1.0 C4 B:O831293 3.2 30.3 1.0 CG1 B:VAL147 3.2 16.6 1.0 O B:LEU145 3.4 15.4 1.0 C B:LEU145 3.4 13.4 1.0 CG2 B:VAL147 3.4 16.9 1.0 C B:TRP146 3.5 14.5 1.0 N B:VAL147 3.6 14.6 1.0 N B:TRP146 3.6 12.8 1.0 CB B:LEU145 3.6 14.1 1.0 CB B:VAL147 3.8 15.7 1.0 CA B:TRP146 3.8 13.5 1.0 O B:TRP146 3.8 15.2 1.0 C1 B:O831293 4.0 31.2 1.0 CA B:LEU145 4.1 12.5 1.0 CA B:VAL147 4.2 15.3 1.0 C10 B:O831293 4.3 30.6 1.0 C3 B:O831293 4.4 31.2 1.0 CD1 B:PHE109 4.5 13.6 1.0 SG B:CYS220 4.6 24.0 0.4 CE1 B:PHE109 4.7 14.6 1.0 C2 B:O831293 4.8 31.4 1.0 C5 B:O831293 4.8 32.4 1.0 SG B:CYS220 4.9 21.7 0.6 CG B:LEU145 4.9 14.9 1.0

M.R.Bauer, R.N.Jones, M.G.J.Baud, R.Wilcken, F.M.Boeckler, A.R.Fersht, A.C.Joerger, J.Spencer. Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions For the Design of P53 Mutant Y220C Rescue Drugs. Acs Chem.Biol. V. 11 2265 2016.
ISSN: ISSN 1554-8929
PubMed: 27267810
DOI: 10.1021/ACSCHEMBIO.6B00315