Fluorine in PDB 8a32: P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769, PDB code: 8a32 was solved by D.I.Balourdas, J.R.Stephenson Clarke, M.G.J.Baud, S.Knapp, A.C.Joerger, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.01 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.119, 71.072, 105.315, 90, 90, 90
R / Rfree (%)	16.4 / 19.3

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	4 atoms

The binding sites of Fluorine atom in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 (pdb code 8a32). 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 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769, PDB code: 8a32:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769


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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:24.8 occ:1.00 F A:KVA401 0.0 24.8 1.0 C6 A:KVA401 1.3 24.0 1.0 C5 A:KVA401 2.4 23.4 1.0 C7 A:KVA401 2.4 25.0 1.0 F1 A:KVA401 2.9 26.1 1.0 CD1 A:LEU145 3.0 22.4 1.0 O A:HOH671 3.2 30.8 1.0 N A:KVA401 3.5 26.4 1.0 C8 A:KVA401 3.5 25.1 1.0 CG2 A:VAL157 3.6 18.2 0.7 CA A:CYS220 3.6 20.7 1.0 SG A:CYS220 3.7 24.6 1.0 CB A:CYS220 3.7 21.9 1.0 CG1 A:VAL157 4.0 15.5 0.3 CG2 A:THR230 4.0 21.3 1.0 N A:GLU221 4.1 22.6 1.0 CG A:LEU145 4.2 18.3 1.0 CB A:LEU145 4.3 16.4 1.0 CB A:THR230 4.3 20.3 1.0 O A:GLU221 4.4 24.4 1.0 C A:CYS220 4.4 22.6 1.0 N A:CYS220 4.7 18.5 1.0 CB A:VAL157 4.7 16.1 0.7 CB A:VAL157 4.8 15.5 0.3 OG1 A:THR230 4.8 21.6 1.0 C4 A:KVA401 4.8 31.6 1.0 O A:PRO219 5.0 18.8 1.0

Fluorine binding site 2 out of 4 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769


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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.1 occ:1.00 F1 A:KVA401 0.0 26.1 1.0 C7 A:KVA401 1.3 25.0 1.0 C8 A:KVA401 2.4 25.1 1.0 C6 A:KVA401 2.4 24.0 1.0 F A:KVA401 2.9 24.8 1.0 CD1 A:LEU257 3.3 17.0 1.0 CG2 A:VAL157 3.4 18.2 0.7 N A:KVA401 3.5 26.4 1.0 C5 A:KVA401 3.5 23.4 1.0 CE1 A:PHE109 3.6 15.4 1.0 CD1 A:LEU145 3.7 22.4 1.0 SG A:CYS220 3.8 24.6 1.0 CB A:LEU145 3.8 16.4 1.0 CD1 A:PHE109 4.0 15.3 1.0 CG A:LEU145 4.3 18.3 1.0 CG A:LEU257 4.6 15.5 1.0 CB A:CYS220 4.7 21.9 1.0 CG1 A:VAL147 4.7 16.6 1.0 CB A:VAL157 4.7 15.5 0.3 CZ A:PHE109 4.7 15.8 1.0 CB A:VAL157 4.8 16.1 0.7 CD2 A:LEU145 4.8 18.8 1.0 C4 A:KVA401 4.8 31.6 1.0 CG1 A:VAL157 4.9 15.5 0.3 CD2 A:LEU257 4.9 15.4 1.0 I1 A:KVA401 5.0 21.3 1.0

Fluorine binding site 3 out of 4 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769


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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:27.1 occ:1.00 F B:KVA401 0.0 27.1 1.0 C6 B:KVA401 1.3 27.4 1.0 C5 B:KVA401 2.4 26.3 1.0 C7 B:KVA401 2.4 27.3 1.0 F1 B:KVA401 2.9 27.4 1.0 CD1 B:LEU145 3.0 26.1 1.0 O B:HOH658 3.4 24.9 1.0 N B:KVA401 3.5 27.7 1.0 C8 B:KVA401 3.5 27.2 1.0 SG B:CYS220 3.6 22.6 1.0 CA B:CYS220 3.6 18.5 1.0 CB B:CYS220 3.6 19.7 1.0 CG2 B:VAL157 3.6 18.0 0.8 CG2 B:THR230 4.1 20.0 1.0 CG1 B:VAL157 4.1 15.2 0.2 N B:GLU221 4.2 22.0 1.0 CG B:LEU145 4.2 21.3 1.0 CB B:LEU145 4.3 19.1 1.0 CB B:THR230 4.3 19.7 1.0 O B:GLU221 4.4 21.7 1.0 C B:CYS220 4.4 22.0 1.0 N B:CYS220 4.7 18.3 1.0 CB B:VAL157 4.8 15.2 0.2 CB B:VAL157 4.8 16.8 0.8 C4 B:KVA401 4.8 33.2 1.0 OG1 B:THR230 4.8 21.6 1.0

Fluorine binding site 4 out of 4 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769


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 Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC769 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:27.4 occ:1.00 F1 B:KVA401 0.0 27.4 1.0 C7 B:KVA401 1.3 27.3 1.0 C8 B:KVA401 2.4 27.2 1.0 C6 B:KVA401 2.4 27.4 1.0 F B:KVA401 2.9 27.1 1.0 CD1 B:LEU257 3.4 17.7 1.0 N B:KVA401 3.5 27.7 1.0 C5 B:KVA401 3.5 26.3 1.0 CE1 B:PHE109 3.6 16.4 1.0 CG2 B:VAL157 3.7 18.0 0.8 CB B:LEU145 3.8 19.1 1.0 CD1 B:LEU145 3.9 26.1 1.0 SG B:CYS220 3.9 22.6 1.0 CD1 B:PHE109 3.9 15.5 1.0 CG B:LEU145 4.3 21.3 1.0 CG1 B:VAL147 4.4 19.3 1.0 CG B:LEU257 4.6 16.1 1.0 CZ B:PHE109 4.7 16.5 1.0 CD2 B:LEU257 4.7 17.4 1.0 CB B:CYS220 4.8 19.7 1.0 CD2 B:LEU145 4.8 21.7 1.0 C4 B:KVA401 4.8 33.2 1.0 I1 B:KVA401 4.9 23.5 1.0 CG B:PRO151 5.0 21.6 1.0

J.R.Stephenson Clarke, L.R.Douglas, P.J.Duriez, D.I.Balourdas, A.C.Joerger, R.Khadiullina, E.Bulatov, M.G.J.Baud. Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic P53 Mutant Y220C. Acs Pharmacol Transl Sci V. 5 1169 2022.
ISSN: ESSN 2575-910
PubMed: 36407959
DOI: 10.1021/ACSPTSCI.2C00164