Fluorine in PDB 8f9d: Compound 21 Bound to Procaspase-6

All present enzymatic activity of Compound 21 Bound to Procaspase-6:
3.4.22.59;

The structure of Compound 21 Bound to Procaspase-6, PDB code: 8f9d 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)	48.46 / 2.65
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	101.529, 101.529, 321.926, 90, 90, 120
R / Rfree (%)	19.3 / 22.9

The binding sites of Fluorine atom in the Compound 21 Bound to Procaspase-6 (pdb code 8f9d). 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 21 Bound to Procaspase-6, PDB code: 8f9d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Compound 21 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 21 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:53.0 occ:0.50 F B:XNK301 0.0 53.0 0.5 C1 B:XNK301 1.4 51.8 0.5 C2 B:XNK301 2.3 49.3 0.5 C6 B:XNK301 2.4 48.1 0.5 C B:SER196 3.5 65.9 1.0 CA B:SER196 3.6 65.4 1.0 C3 B:XNK301 3.6 52.4 0.5 N B:SER196 3.7 67.5 1.0 O B:SER196 3.7 71.1 1.0 C5 B:XNK301 3.7 47.4 0.5 C B:ALA195 3.8 63.5 1.0 O B:ALA195 3.9 68.3 1.0 N B:VAL197 3.9 62.7 1.0 CA B:GLU214 4.0 72.8 1.0 O B:VAL197 4.1 66.1 1.0 C4 B:XNK301 4.2 54.2 0.5 CB B:ALA195 4.2 63.0 1.0 CB B:GLU214 4.3 82.9 1.0 C B:VAL197 4.3 59.8 1.0 N B:GLU214 4.5 66.5 1.0 CA B:ALA195 4.6 60.0 1.0 CG B:GLU214 4.7 86.0 1.0 O1 B:XNK301 4.7 45.7 0.5 CA B:VAL197 4.7 62.2 1.0 N B:TYR198 4.7 56.7 1.0 CD1 B:TYR198 4.8 61.4 1.0

Fluorine binding site 2 out of 4 in the Compound 21 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 21 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:55.1 occ:0.50 F B:XNK301 0.0 55.1 0.5 C1 B:XNK301 1.4 54.0 0.5 C2 B:XNK301 2.4 50.2 0.5 C6 B:XNK301 2.4 51.0 0.5 C A:SER196 3.4 66.5 1.0 CA A:SER196 3.4 66.2 1.0 O A:SER196 3.5 68.8 1.0 N A:SER196 3.6 65.4 1.0 C3 B:XNK301 3.6 54.1 0.5 C A:ALA195 3.7 61.2 1.0 O A:ALA195 3.7 70.1 1.0 C5 B:XNK301 3.7 48.9 0.5 N A:VAL197 3.9 64.3 1.0 CA A:GLU214 4.1 74.3 1.0 C4 B:XNK301 4.2 56.1 0.5 CB A:ALA195 4.2 68.1 1.0 O A:VAL197 4.3 70.5 1.0 CB A:GLU214 4.4 81.9 1.0 C A:VAL197 4.5 61.1 1.0 O A:HOH329 4.5 61.4 1.0 CA A:ALA195 4.6 63.2 1.0 CG A:GLU214 4.6 83.3 1.0 N A:GLU214 4.7 68.0 1.0 O1 B:XNK301 4.7 45.6 0.5 CA A:VAL197 4.8 63.8 1.0 CD1 A:TYR198 4.8 65.4 1.0 CB A:SER196 4.9 64.6 1.0 N A:TYR198 4.9 58.0 1.0

Fluorine binding site 3 out of 4 in the Compound 21 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 21 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:44.6 occ:0.50 F D:XNK301 0.0 44.6 0.5 C1 D:XNK301 1.3 42.3 0.5 C6 D:XNK301 2.3 39.8 0.5 C2 D:XNK301 2.4 41.4 0.5 C D:SER196 3.2 66.0 1.0 N D:SER196 3.2 67.0 1.0 N D:VAL197 3.4 62.1 1.0 CA D:SER196 3.4 66.9 1.0 C D:ALA195 3.4 62.5 1.0 O D:VAL197 3.6 63.7 1.0 C5 D:XNK301 3.6 41.6 0.5 CB D:ALA195 3.7 65.1 1.0 C3 D:XNK301 3.7 43.0 0.5 O D:SER196 3.7 79.5 1.0 O D:ALA195 3.8 61.7 1.0 C D:VAL197 3.9 62.3 1.0 CA D:GLU214 4.0 67.6 1.0 C4 D:XNK301 4.1 41.8 0.5 CA D:ALA195 4.1 60.4 1.0 CA D:VAL197 4.3 63.4 1.0 N D:GLU214 4.3 64.4 1.0 CB D:GLU214 4.4 71.0 1.0 N D:TYR198 4.5 56.5 1.0 O D:HOH405 4.5 48.1 1.0 C D:ALA213 4.8 58.2 1.0 O1 D:XNK301 4.8 38.1 0.5 CG D:GLU214 4.9 79.2 1.0 CB D:SER196 4.9 67.9 1.0 O D:ALA213 4.9 55.8 1.0 CD1 D:TYR198 4.9 55.3 1.0 CA D:TYR198 5.0 54.6 1.0

Fluorine binding site 4 out of 4 in the Compound 21 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 21 Bound to Procaspase-6 within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:46.3 occ:0.50 F D:XNK301 0.0 46.3 0.5 C1 D:XNK301 1.3 45.9 0.5 C6 D:XNK301 2.4 43.1 0.5 C2 D:XNK301 2.4 44.6 0.5 C C:SER196 3.3 62.9 1.0 N C:SER196 3.3 66.1 1.0 CA C:SER196 3.4 65.4 1.0 N C:VAL197 3.4 62.3 1.0 C C:ALA195 3.5 62.1 1.0 O C:VAL197 3.6 61.6 1.0 C5 D:XNK301 3.6 45.9 0.5 C3 D:XNK301 3.7 46.6 0.5 CB C:ALA195 3.7 68.7 1.0 O C:SER196 3.7 75.0 1.0 O C:ALA195 3.8 59.5 1.0 C C:VAL197 3.9 60.9 1.0 CA C:GLU214 4.0 66.8 1.0 O C:HOH409 4.1 67.1 1.0 C4 D:XNK301 4.1 45.0 0.5 CA C:ALA195 4.2 62.7 1.0 N C:GLU214 4.3 63.0 1.0 CA C:VAL197 4.3 60.2 1.0 CB C:GLU214 4.4 71.1 1.0 N C:TYR198 4.5 56.5 1.0 C C:ALA213 4.8 59.5 1.0 O1 D:XNK301 4.8 43.3 0.5 CG C:GLU214 4.9 78.2 1.0 O C:ALA213 4.9 58.1 1.0 CB C:SER196 4.9 68.5 1.0 CA C:TYR198 5.0 56.6 1.0 CD1 C:TYR198 5.0 53.5 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.