Fluorine in PDB 8f97: Compound 5 Bound to Procaspase-6

All present enzymatic activity of Compound 5 Bound to Procaspase-6:
3.4.22.59;

The structure of Compound 5 Bound to Procaspase-6, PDB code: 8f97 was solved by P.Fan, Y.Zhao, A.R.Renslo, M.R.Arkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.96 / 2.32
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	102.66, 102.66, 322.767, 90, 90, 120
R / Rfree (%)	17.9 / 21

The structure of Compound 5 Bound to Procaspase-6 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Compound 5 Bound to Procaspase-6 (pdb code 8f97). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Compound 5 Bound to Procaspase-6, PDB code: 8f97:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Compound 5 Bound to Procaspase-6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Compound 5 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:54.3 occ:0.50 F A:XM6301 0.0 54.3 0.5 C11 A:XM6301 1.3 58.1 0.5 C12 A:XM6301 2.3 50.8 0.5 C10 A:XM6301 2.4 52.7 0.5 N A:SER196 3.3 63.9 1.0 C A:SER196 3.4 57.2 1.0 C A:ALA195 3.5 57.8 1.0 C13 A:XM6301 3.5 45.8 0.5 CA A:SER196 3.5 59.5 1.0 C9 A:XM6301 3.6 49.9 0.5 N A:VAL197 3.7 57.2 1.0 CB A:ALA195 3.7 56.5 1.0 O A:VAL197 3.7 57.3 1.0 O A:ALA195 3.8 62.5 1.0 O A:SER196 3.8 65.3 1.0 CA A:GLU214 3.9 64.0 1.0 C A:VAL197 4.0 51.4 1.0 O A:HOH447 4.0 57.2 1.0 C8 A:XM6301 4.1 50.9 0.5 CA A:ALA195 4.2 55.0 1.0 N A:GLU214 4.2 59.0 1.0 CB A:GLU214 4.2 67.5 1.0 CA A:VAL197 4.5 57.3 1.0 O A:XM6301 4.6 48.3 0.5 N A:TYR198 4.6 51.0 1.0 C A:ALA213 4.7 55.6 1.0 O A:HOH408 4.8 52.1 1.0 CG A:GLU214 4.9 76.1 1.0 CA A:TYR198 5.0 51.8 1.0 CD1 A:TYR198 5.0 52.5 1.0

Fluorine binding site 2 out of 4 in the Compound 5 Bound to Procaspase-6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Compound 5 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:48.7 occ:0.50 F A:XM6301 0.0 48.7 0.5 C11 A:XM6301 1.3 56.6 0.5 C12 A:XM6301 2.3 45.5 0.5 C10 A:XM6301 2.4 55.5 0.5 N B:SER196 3.4 59.2 1.0 C13 A:XM6301 3.5 45.3 0.5 C B:SER196 3.5 60.7 1.0 O B:VAL197 3.5 54.6 1.0 C B:ALA195 3.7 56.7 1.0 N B:VAL197 3.7 56.5 1.0 C9 A:XM6301 3.7 52.5 0.5 CA B:SER196 3.7 60.7 1.0 CB B:ALA195 3.8 55.5 1.0 CA B:GLU214 3.8 64.7 1.0 C B:VAL197 3.9 54.2 1.0 O B:SER196 3.9 60.7 1.0 N B:GLU214 4.0 59.5 1.0 O B:ALA195 4.0 62.5 1.0 CB B:GLU214 4.1 62.4 1.0 C8 A:XM6301 4.1 54.2 0.5 CA B:ALA195 4.3 55.9 1.0 CA B:VAL197 4.5 55.9 1.0 N B:TYR198 4.5 52.9 1.0 O A:XM6301 4.6 50.3 0.5 C B:ALA213 4.6 54.3 1.0 O B:HOH415 4.7 47.8 1.0 CA B:TYR198 4.8 53.9 1.0 O B:HOH445 4.9 51.8 1.0 CG B:GLU214 4.9 72.9 1.0 O B:ALA213 4.9 57.0 1.0 CD1 B:TYR198 5.0 53.3 1.0

Fluorine binding site 3 out of 4 in the Compound 5 Bound to Procaspase-6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Compound 5 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:49.0 occ:0.50 F C:XM6301 0.0 49.0 0.5 C11 C:XM6301 1.4 59.0 0.5 C12 C:XM6301 2.3 48.7 0.5 C10 C:XM6301 2.5 58.1 0.5 N C:SER196 3.5 59.7 1.0 C C:SER196 3.6 57.4 1.0 C13 C:XM6301 3.6 47.8 0.5 O C:VAL197 3.7 60.6 1.0 CA C:GLU214 3.7 64.8 1.0 C C:ALA195 3.7 57.1 1.0 N C:VAL197 3.7 54.4 1.0 CA C:SER196 3.8 58.1 1.0 C9 C:XM6301 3.8 54.1 0.5 CB C:ALA195 3.8 58.1 1.0 CB C:GLU214 3.9 65.1 1.0 O C:SER196 4.0 63.6 1.0 N C:GLU214 4.0 60.2 1.0 C C:VAL197 4.0 51.9 1.0 O C:ALA195 4.1 69.8 1.0 O C:HOH463 4.1 59.1 1.0 C8 C:XM6301 4.2 58.2 0.5 CA C:ALA195 4.4 56.4 1.0 O C:HOH469 4.5 65.7 1.0 CA C:VAL197 4.6 53.1 1.0 C C:ALA213 4.6 55.9 1.0 O C:XM6301 4.6 50.8 0.5 N C:TYR198 4.6 46.8 1.0 O C:HOH404 4.7 59.6 1.0 CG C:GLU214 4.7 79.1 1.0 O C:ALA213 4.9 53.8 1.0 O C:HOH405 4.9 52.2 1.0 O C:HOH428 5.0 60.3 1.0 CA C:TYR198 5.0 54.8 1.0

Fluorine binding site 4 out of 4 in the Compound 5 Bound to Procaspase-6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Compound 5 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:52.2 occ:0.50 F C:XM6301 0.0 52.2 0.5 C11 C:XM6301 1.4 57.2 0.5 C12 C:XM6301 2.3 47.4 0.5 C10 C:XM6301 2.5 54.9 0.5 N D:SER196 3.4 59.1 1.0 C D:SER196 3.5 60.7 1.0 C13 C:XM6301 3.6 48.8 0.5 C D:ALA195 3.6 58.7 1.0 CA D:SER196 3.6 55.5 1.0 C9 C:XM6301 3.8 54.0 0.5 N D:VAL197 3.8 53.8 1.0 CA D:GLU214 3.8 62.8 1.0 O D:SER196 3.8 61.5 1.0 O D:VAL197 3.8 55.5 1.0 CB D:ALA195 3.9 55.2 1.0 O D:ALA195 3.9 63.2 1.0 O D:HOH465 4.0 59.6 1.0 CB D:GLU214 4.0 70.3 1.0 C D:VAL197 4.2 50.1 1.0 C8 C:XM6301 4.2 53.8 0.5 N D:GLU214 4.2 59.2 1.0 O D:HOH466 4.3 68.7 1.0 CA D:ALA195 4.4 51.9 1.0 CA D:VAL197 4.6 52.2 1.0 O C:XM6301 4.7 47.5 0.5 CG D:GLU214 4.7 80.8 1.0 N D:TYR198 4.7 48.5 1.0 C D:ALA213 4.8 60.0 1.0 CD1 D:TYR198 5.0 59.9 1.0 O C:HOH403 5.0 58.7 1.0

P.Fan, Y.Zhao, A.R.Renslo, M.R.Arkin. A Comprehensive Empirical-Computational Study of Diverse Heteroarene Stacking Interactions Under Physiological Conditions To Be Published.