Fluorine in PDB 8a31: P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694, PDB code: 8a31 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)	47.98 / 1.46
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.981, 71.063, 105.089, 90, 90, 90
R / Rfree (%)	15.7 / 19.1

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 also contains other interesting chemical elements:

Iodine	(I)	6 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 (pdb code 8a31). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694, PDB code: 8a31:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


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 JC694 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:20.1 occ:0.74 F A:KV0401 0.0 20.1 0.7 C7 A:KV0401 1.4 19.1 0.7 C8 A:KV0401 1.4 38.3 0.3 C9 A:KV0401 2.4 39.3 0.3 C6 A:KV0401 2.4 18.8 0.7 C8 A:KV0401 2.5 18.6 0.7 C7 A:KV0401 2.5 37.8 0.3 F A:KV0401 3.1 36.4 0.3 CD1 A:LEU257 3.3 15.1 1.0 CG2 A:VAL157 3.4 18.3 1.0 CE1 A:PHE109 3.5 14.0 1.0 N A:KV0401 3.5 18.9 0.7 N A:KV0401 3.5 40.9 0.3 C9 A:KV0401 3.5 17.6 0.7 C6 A:KV0401 3.6 39.0 0.3 CD1 A:LEU145 3.6 18.4 1.0 CB A:LEU145 3.8 14.0 1.0 SG A:CYS220 3.8 22.6 1.0 CD1 A:PHE109 3.9 14.4 1.0 CG A:LEU145 4.2 15.6 1.0 CG1 A:VAL147 4.6 15.0 1.0 CG A:LEU257 4.6 14.3 1.0 CZ A:PHE109 4.6 14.3 1.0 CB A:CYS220 4.7 19.6 1.0 CD2 A:LEU145 4.8 15.8 1.0 CB A:VAL157 4.9 14.7 1.0 C5 A:KV0401 4.9 23.5 0.7 C5 A:KV0401 4.9 44.4 0.3 CD2 A:LEU257 4.9 14.3 1.0 I1 A:KV0401 4.9 14.9 0.7 I1 A:KV0401 5.0 48.6 0.3

Fluorine binding site 2 out of 3 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


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 JC694 within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.4 occ:0.26 F A:KV0401 0.0 36.4 0.3 C8 A:KV0401 1.3 18.6 0.7 C7 A:KV0401 1.4 37.8 0.3 C9 A:KV0401 2.3 17.6 0.7 C6 A:KV0401 2.4 39.0 0.3 C8 A:KV0401 2.5 38.3 0.3 C7 A:KV0401 2.5 19.1 0.7 O A:HOH663 2.8 22.5 1.0 F A:KV0401 3.1 20.1 0.7 CD1 A:LEU145 3.1 18.4 1.0 CA A:CYS220 3.4 18.6 1.0 N A:KV0401 3.5 18.9 0.7 N A:KV0401 3.5 40.9 0.3 C9 A:KV0401 3.5 39.3 0.3 C6 A:KV0401 3.5 18.8 0.7 CG2 A:VAL157 3.6 18.3 1.0 CB A:CYS220 3.6 19.6 1.0 SG A:CYS220 3.7 22.6 1.0 N A:GLU221 3.9 21.4 1.0 CG2 A:THR230 4.1 18.1 1.0 C A:CYS220 4.2 20.6 1.0 O A:GLU221 4.3 22.0 1.0 CG A:LEU145 4.4 15.6 1.0 CB A:THR230 4.4 17.4 1.0 N A:CYS220 4.5 17.4 1.0 CB A:LEU145 4.5 14.0 1.0 O A:PRO219 4.7 17.3 1.0 CB A:VAL157 4.7 14.7 1.0 C5 A:KV0401 4.8 23.5 0.7 C5 A:KV0401 4.9 44.4 0.3 OG1 A:THR230 4.9 19.0 1.0 C A:PRO219 5.0 16.4 1.0

Fluorine binding site 3 out of 3 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


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 JC694 within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:28.4 occ:1.00 F B:KV0401 0.0 28.4 1.0 C7 B:KV0401 1.4 27.0 1.0 C6 B:KV0401 2.4 26.6 1.0 C8 B:KV0401 2.5 26.4 1.0 CD1 B:LEU257 3.3 16.0 1.0 N B:KV0401 3.5 27.2 1.0 C9 B:KV0401 3.5 25.2 1.0 CE1 B:PHE109 3.5 15.8 1.0 CG2 B:VAL157 3.6 14.3 0.7 CD1 B:LEU145 3.7 21.6 1.0 CB B:LEU145 3.8 15.8 1.0 SG B:CYS220 3.9 20.5 1.0 CD1 B:PHE109 3.9 14.4 1.0 CG B:LEU145 4.3 17.9 1.0 CG1 B:VAL147 4.4 16.8 1.0 CG B:LEU257 4.6 14.4 1.0 CZ B:PHE109 4.7 15.2 1.0 CD2 B:LEU257 4.7 15.4 1.0 CB B:CYS220 4.8 17.5 1.0 CD2 B:LEU145 4.8 18.0 1.0 C5 B:KV0401 4.9 31.4 1.0 I1 B:KV0401 4.9 20.9 1.0 CB B:VAL157 5.0 13.1 0.3

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