Fluorine in PDB 8a6f: Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3

All present enzymatic activity of Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3:
2.7.11.1;

The structure of Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3, PDB code: 8a6f was solved by D.N.Kenanova, E.J.Visser, J.Virta, E.Sijbesma, F.Centorrino, M.Zhong, H.Vickery, J.Neitz, L.Brunsveld, C.Ottmann, M.R.Arkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.77 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.944, 112.909, 62.794, 90, 90, 90
R / Rfree (%)	16.2 / 18.1

The structure of Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3 (pdb code 8a6f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3, PDB code: 8a6f:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:32.4 occ:1.00 F1 A:O56304 0.0 32.4 1.0 C12 A:O56304 1.4 36.0 1.0 F3 A:O56304 2.2 38.2 1.0 F2 A:O56304 2.2 34.3 1.0 C11 A:O56304 2.4 30.2 1.0 HG13 A:ILE219 2.5 24.9 1.0 HG12 A:ILE219 2.7 24.9 1.0 CL A:O56304 2.7 46.1 1.0 C13 A:O56304 2.9 32.6 1.0 HB3 A:LEU218 3.0 24.1 1.0 CG1 A:ILE219 3.1 20.8 1.0 HB2 A:LEU218 3.3 24.1 1.0 C10 A:O56304 3.5 29.4 1.0 CB A:LEU218 3.6 20.1 1.0 HA A:ILE219 3.7 19.9 1.0 N A:ILE219 3.7 15.9 1.0 HD11 A:ILE219 3.7 28.8 1.0 H A:ILE219 3.8 19.1 1.0 H17 A:O56304 3.9 35.2 1.0 C A:LEU218 4.0 18.2 1.0 CD1 A:ILE219 4.0 24.0 1.0 CA A:ILE219 4.0 16.6 1.0 HD13 A:LEU218 4.1 47.4 1.0 HD11 A:LEU222 4.1 22.9 1.0 CB A:ILE219 4.1 18.3 1.0 C14 A:O56304 4.2 29.8 1.0 HG21 P:VAL263 4.2 36.0 1.0 HG2 P:PRO261 4.3 26.4 1.0 HD2 P:PRO261 4.3 24.2 1.0 HD12 A:LEU222 4.3 22.9 1.0 O A:ASP215 4.4 21.8 1.0 O A:LEU218 4.4 19.9 1.0 CA A:LEU218 4.4 20.1 1.0 HD12 A:LEU218 4.5 47.4 1.0 HD13 A:ILE219 4.6 28.8 1.0 HG3 P:PRO261 4.6 26.4 1.0 CD1 A:LEU218 4.6 39.5 1.0 HD12 A:ILE219 4.7 28.8 1.0 C9 A:O56304 4.7 26.8 1.0 CD1 A:LEU222 4.7 19.1 1.0 CG A:LEU218 4.7 34.8 1.0 HG23 P:VAL263 4.7 36.0 1.0 HG22 P:VAL263 4.8 36.0 1.0 HB A:ILE219 4.8 22.0 1.0 CG P:PRO261 4.8 22.0 1.0 CG2 P:VAL263 4.8 30.0 1.0 HG21 A:ILE219 4.9 24.1 1.0 H16 A:O56304 4.9 35.7 1.0 C15 A:O56304 4.9 30.5 1.0 CD P:PRO261 4.9 20.2 1.0 HG23 P:THR260 4.9 25.5 1.0

Fluorine binding site 2 out of 3 in the Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:34.3 occ:1.00 F2 A:O56304 0.0 34.3 1.0 C12 A:O56304 1.4 36.0 1.0 F1 A:O56304 2.2 32.4 1.0 F3 A:O56304 2.3 38.2 1.0 C11 A:O56304 2.4 30.2 1.0 H17 A:O56304 2.4 35.2 1.0 HD2 P:PRO261 2.4 24.2 1.0 C10 A:O56304 2.7 29.4 1.0 HG2 P:PRO261 2.8 26.4 1.0 HG12 A:ILE219 2.9 24.9 1.0 HG23 P:THR260 2.9 25.5 1.0 CD P:PRO261 3.2 20.2 1.0 CG P:PRO261 3.4 22.0 1.0 HG23 P:VAL263 3.6 36.0 1.0 C13 A:O56304 3.7 32.6 1.0 CG1 A:ILE219 3.7 20.8 1.0 HG3 P:PRO261 3.7 26.4 1.0 HG13 A:ILE219 3.7 24.9 1.0 CG2 P:THR260 3.7 21.2 1.0 HD11 A:LEU222 3.8 22.9 1.0 HG22 P:THR260 3.8 25.5 1.0 HD3 P:PRO261 3.8 24.2 1.0 HG21 P:VAL263 3.9 36.0 1.0 H10 A:O56304 3.9 33.0 1.0 HD11 A:ILE219 4.0 28.8 1.0 HD12 A:LEU222 4.0 22.9 1.0 HG22 P:VAL263 4.0 36.0 1.0 CG2 P:VAL263 4.1 30.0 1.0 HG21 P:THR260 4.1 25.5 1.0 O P:PRO261 4.1 21.0 1.0 C9 A:O56304 4.1 26.8 1.0 N P:PRO261 4.2 17.4 1.0 HA P:THR260 4.2 18.9 1.0 CD1 A:ILE219 4.3 24.0 1.0 CD1 A:LEU222 4.3 19.1 1.0 HD13 A:ILE219 4.4 28.8 1.0 CL A:O56304 4.4 46.1 1.0 O1 A:O56304 4.5 27.5 1.0 HA A:ILE219 4.5 19.9 1.0 O A:HOH417 4.5 24.8 1.0 HG21 A:ILE219 4.7 24.1 1.0 HD13 A:LEU222 4.7 22.9 1.0 CB P:PRO261 4.7 20.7 1.0 C14 A:O56304 4.8 29.8 1.0 C P:PRO261 4.8 19.6 1.0 CB A:ILE219 4.8 18.3 1.0 CA P:PRO261 4.9 19.9 1.0 CA P:THR260 4.9 15.7 1.0 CB P:THR260 4.9 19.0 1.0 C P:THR260 4.9 18.2 1.0 C15 A:O56304 5.0 30.5 1.0

Fluorine binding site 3 out of 3 in the Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Small Molecule Stabilizer (Compound 8) For C-Raf and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:38.2 occ:1.00 F3 A:O56304 0.0 38.2 1.0 C12 A:O56304 1.4 36.0 1.0 F1 A:O56304 2.2 32.4 1.0 F2 A:O56304 2.3 34.3 1.0 C11 A:O56304 2.4 30.2 1.0 HG21 P:VAL263 2.6 36.0 1.0 HG22 P:VAL263 2.6 36.0 1.0 CG2 P:VAL263 2.9 30.0 1.0 HG2 P:PRO261 2.9 26.4 1.0 HG23 P:VAL263 3.1 36.0 1.0 C13 A:O56304 3.1 32.6 1.0 CL A:O56304 3.3 46.1 1.0 C10 A:O56304 3.3 29.4 1.0 H17 A:O56304 3.5 35.2 1.0 CG P:PRO261 3.8 22.0 1.0 HG3 P:PRO261 3.8 26.4 1.0 HD2 P:PRO261 4.0 24.2 1.0 HD13 A:LEU218 4.3 47.4 1.0 HB3 A:LEU218 4.3 24.1 1.0 C14 A:O56304 4.3 29.8 1.0 CB P:VAL263 4.4 29.2 1.0 HG12 A:ILE219 4.5 24.9 1.0 CD P:PRO261 4.5 20.2 1.0 C9 A:O56304 4.5 26.8 1.0 HG13 A:ILE219 4.6 24.9 1.0 HG11 P:VAL263 4.7 38.6 1.0 O P:PRO261 4.8 21.0 1.0 HG13 P:VAL263 4.8 38.6 1.0 HD11 A:LEU222 4.8 22.9 1.0 O P:ASN262 4.8 23.4 1.0 HB2 A:LEU218 4.9 24.1 1.0 CG1 P:VAL263 4.9 32.1 1.0 HB P:VAL263 4.9 35.0 1.0 HA P:VAL263 4.9 35.1 1.0 HB2 P:PRO261 4.9 24.9 1.0 C15 A:O56304 4.9 30.5 1.0 CB P:PRO261 5.0 20.7 1.0 CG1 A:ILE219 5.0 20.8 1.0

D.N.Kenanova, E.J.Visser, J.M.Virta, E.Sijbesma, F.Centorrino, H.R.Vickery, M.Zhong, R.J.Neitz, L.Brunsveld, C.Ottmann, M.R.Arkin. A Systematic Approach to the Discovery of Protein–Protein Interaction Stabilizers Acs Cent.Sci. 2023.
ISSN: ESSN 2374-7951
DOI: 10.1021/ACSCENTSCI.2C01449