Fluorine in PDB 8a6h: Small Molecule Stabilizer (Compound 7) For C-Raf and 14-3-3

All present enzymatic activity of Small Molecule Stabilizer (Compound 7) For C-Raf and 14-3-3:
2.7.11.1;

The structure of Small Molecule Stabilizer (Compound 7) For C-Raf and 14-3-3, PDB code: 8a6h 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)	45.63 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.499, 112.234, 62.756, 90, 90, 90
R / Rfree (%)	15.3 / 17.4

The structure of Small Molecule Stabilizer (Compound 7) For C-Raf and 14-3-3 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Small Molecule Stabilizer (Compound 7) For C-Raf and 14-3-3 (pdb code 8a6h). 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 7) For C-Raf and 14-3-3, PDB code: 8a6h:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Small Molecule Stabilizer (Compound 7) 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 7) For C-Raf and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:32.9 occ:1.00 F15 A:L6L304 0.0 32.9 1.0 C14 A:L6L304 1.3 32.8 1.0 F17 A:L6L304 2.2 47.8 1.0 F16 A:L6L304 2.3 34.7 1.0 C13 A:L6L304 2.3 30.3 1.0 H181 A:L6L304 2.4 34.4 1.0 HB3 A:LEU218 2.6 15.9 1.0 C18 A:L6L304 2.7 28.7 1.0 HG13 A:ILE219 2.8 18.0 1.0 O A:ASP215 2.8 16.8 1.0 HA A:ASP215 3.0 20.8 1.0 HD22 A:LEU218 3.1 39.1 1.0 HD13 A:LEU218 3.2 33.3 1.0 HD13 A:ILE219 3.3 20.1 1.0 C12 A:L6L304 3.5 26.2 1.0 CB A:LEU218 3.5 13.2 1.0 CG1 A:ILE219 3.6 15.0 1.0 C A:ASP215 3.6 16.1 1.0 CA A:ASP215 3.7 17.4 1.0 HB3 A:ASP215 3.8 23.0 1.0 HG12 A:ILE219 3.8 18.0 1.0 H121 A:L6L304 3.9 31.4 1.0 HB2 A:LEU218 3.9 15.9 1.0 CD2 A:LEU218 3.9 32.6 1.0 CD1 A:ILE219 3.9 16.8 1.0 H A:ILE219 3.9 14.8 1.0 C19 A:L6L304 4.0 31.2 1.0 CG A:LEU218 4.0 28.4 1.0 CD1 A:LEU218 4.0 27.7 1.0 HD21 A:LEU218 4.1 39.1 1.0 HD11 A:ILE219 4.2 20.1 1.0 HG21 P:VAL263 4.2 32.6 1.0 CB A:ASP215 4.2 19.2 1.0 N A:ILE219 4.3 12.3 1.0 HB3 A:PRO167 4.5 13.7 1.0 C11 A:L6L304 4.5 24.7 1.0 HD12 A:LEU218 4.5 33.3 1.0 H A:LEU218 4.6 16.1 1.0 OD1 A:ASP215 4.6 26.2 1.0 CA A:LEU218 4.6 15.1 1.0 H191 A:L6L304 4.6 37.4 1.0 HD23 A:LEU218 4.7 39.1 1.0 HD11 A:LEU218 4.7 33.3 1.0 O A:LYS214 4.7 17.5 1.0 HD12 A:ILE219 4.7 20.1 1.0 C A:LEU218 4.7 12.7 1.0 C20 A:L6L304 4.8 25.3 1.0 CG A:ASP215 4.8 27.2 1.0 CB A:ILE219 4.8 12.1 1.0 N A:SER216 4.9 13.4 1.0 N A:ASP215 4.9 16.1 1.0 HG A:LEU218 5.0 34.1 1.0 N A:LEU218 5.0 13.5 1.0

Fluorine binding site 2 out of 3 in the Small Molecule Stabilizer (Compound 7) 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 7) For C-Raf and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:34.7 occ:1.00 F16 A:L6L304 0.0 34.7 1.0 C14 A:L6L304 1.4 32.8 1.0 F17 A:L6L304 2.2 47.8 1.0 F15 A:L6L304 2.3 32.9 1.0 C13 A:L6L304 2.4 30.3 1.0 H121 A:L6L304 2.5 31.4 1.0 C12 A:L6L304 2.8 26.2 1.0 HD22 A:LEU218 2.9 39.1 1.0 HG12 A:ILE219 2.9 18.0 1.0 HG13 A:ILE219 3.0 18.0 1.0 HG21 P:VAL263 3.1 32.6 1.0 HD13 A:ILE219 3.2 20.1 1.0 CG1 A:ILE219 3.3 15.0 1.0 HD21 A:LEU218 3.5 39.1 1.0 CD2 A:LEU218 3.6 32.6 1.0 C18 A:L6L304 3.6 28.7 1.0 CD1 A:ILE219 3.7 16.8 1.0 CG2 P:VAL263 3.7 27.2 1.0 HG22 P:VAL263 3.8 32.6 1.0 HG23 P:VAL263 3.8 32.6 1.0 HG2 P:PRO261 3.8 22.1 1.0 HD13 A:LEU218 3.9 33.3 1.0 HB3 A:LEU218 3.9 15.9 1.0 H181 A:L6L304 3.9 34.4 1.0 HD2 P:PRO261 4.0 16.8 1.0 C11 A:L6L304 4.2 24.7 1.0 HD12 A:ILE219 4.2 20.1 1.0 HD23 A:LEU218 4.3 39.1 1.0 HG22 P:THR260 4.3 20.4 1.0 HD11 A:ILE219 4.5 20.1 1.0 CG P:PRO261 4.5 18.4 1.0 CG A:LEU218 4.5 28.4 1.0 HG3 P:PRO261 4.6 22.1 1.0 CD1 A:LEU218 4.6 27.7 1.0 O21 A:L6L304 4.6 21.9 1.0 CB A:LEU218 4.7 13.2 1.0 CD P:PRO261 4.7 14.0 1.0 CB A:ILE219 4.7 12.1 1.0 HA A:ILE219 4.7 14.6 1.0 O A:ASP215 4.7 16.8 1.0 H A:ILE219 4.8 14.8 1.0 C19 A:L6L304 4.8 31.2 1.0 HD11 A:LEU218 4.9 33.3 1.0 N A:ILE219 4.9 12.3 1.0 C20 A:L6L304 5.0 25.3 1.0 HG11 P:VAL263 5.0 35.6 1.0

Fluorine binding site 3 out of 3 in the Small Molecule Stabilizer (Compound 7) 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 7) For C-Raf and 14-3-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:47.8 occ:1.00 F17 A:L6L304 0.0 47.8 1.0 C14 A:L6L304 1.4 32.8 1.0 F15 A:L6L304 2.2 32.9 1.0 F16 A:L6L304 2.2 34.7 1.0 C13 A:L6L304 2.3 30.3 1.0 HG21 P:VAL263 2.5 32.6 1.0 HD13 A:LEU218 2.8 33.3 1.0 H181 A:L6L304 2.9 34.4 1.0 C18 A:L6L304 3.0 28.7 1.0 HG22 P:VAL263 3.0 32.6 1.0 CG2 P:VAL263 3.2 27.2 1.0 C12 A:L6L304 3.4 26.2 1.0 HG11 P:VAL263 3.5 35.6 1.0 H121 A:L6L304 3.6 31.4 1.0 HD22 A:LEU218 3.6 39.1 1.0 CD1 A:LEU218 3.7 27.7 1.0 HG23 P:VAL263 3.8 32.6 1.0 HD21 A:LEU218 3.8 39.1 1.0 HB3 A:LEU218 3.9 15.9 1.0 HD11 A:LEU218 4.0 33.3 1.0 HG13 P:VAL263 4.1 35.6 1.0 CD2 A:LEU218 4.1 32.6 1.0 CG1 P:VAL263 4.1 29.6 1.0 C19 A:L6L304 4.2 31.2 1.0 CB P:VAL263 4.2 25.8 1.0 CG A:LEU218 4.3 28.4 1.0 HD12 A:LEU218 4.3 33.3 1.0 HA A:ASP215 4.4 20.8 1.0 C11 A:L6L304 4.5 24.7 1.0 HG13 A:ILE219 4.5 18.0 1.0 CB A:LEU218 4.6 13.2 1.0 HG2 P:PRO261 4.7 22.1 1.0 HD13 A:ILE219 4.7 20.1 1.0 HB P:VAL263 4.8 31.0 1.0 HB2 A:LEU218 4.8 15.9 1.0 C20 A:L6L304 4.8 25.3 1.0 H191 A:L6L304 5.0 37.4 1.0 O A:ASP215 5.0 16.8 1.0 HG12 A:ILE219 5.0 18.0 1.0 HG12 P:VAL263 5.0 35.6 1.0 HD23 A:LEU218 5.0 39.1 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