Fluorine in PDB 4bpv: Mouse Cathepsin S with Covalent Ligand

All present enzymatic activity of Mouse Cathepsin S with Covalent Ligand:
3.4.22.27;

The structure of Mouse Cathepsin S with Covalent Ligand, PDB code: 4bpv was solved by D.W.Banner, J.Benz, B.Gsell, M.Stihle, A.Ruf, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.11 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.855, 128.917, 97.132, 90.00, 97.44, 90.00
R / Rfree (%)	21.225 / 25.537

The structure of Mouse Cathepsin S with Covalent Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Fluorine atom in the Mouse Cathepsin S with Covalent Ligand (pdb code 4bpv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 30 binding sites of Fluorine where determined in the Mouse Cathepsin S with Covalent Ligand, PDB code: 4bpv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:20.1 occ:1.00 F31 A:OFH1341 0.0 20.1 1.0 C8 A:OFH1341 1.3 22.8 1.0 F33 A:OFH1341 2.1 26.9 1.0 F32 A:OFH1341 2.1 21.2 1.0 C1 A:OFH1341 2.4 21.2 1.0 N A:GLY192 3.0 19.9 1.0 C4 A:OFH1341 3.1 21.3 1.0 C12 A:OFH1341 3.2 21.9 1.0 CE2 A:TYR193 3.3 24.3 1.0 CA A:GLY192 3.3 19.1 1.0 C9 A:OFH1341 3.3 20.7 1.0 CZ A:TYR193 3.3 23.8 1.0 N3 A:OFH1341 3.4 21.4 1.0 O A:GLY192 3.5 19.1 1.0 C A:GLY192 3.5 19.1 1.0 OH A:TYR193 3.6 24.4 1.0 C A:GLY191 3.7 20.2 1.0 CD2 A:TYR193 3.8 22.9 1.0 CE1 A:TYR193 3.8 24.5 1.0 C11 A:OFH1341 3.8 22.2 1.0 O27 A:OFH1341 3.9 21.2 1.0 CG A:TYR193 4.2 22.5 1.0 CD1 A:TYR193 4.2 24.2 1.0 O A:GLY191 4.3 19.3 1.0 O30 A:OFH1341 4.3 18.9 1.0 N A:TYR193 4.4 19.7 1.0 CA A:GLY191 4.4 21.1 1.0 CE A:LYS187 4.5 29.1 1.0 C7 A:OFH1341 4.6 19.9 1.0 O A:HOH2097 4.7 29.5 1.0 C5 A:OFH1341 4.7 21.3 1.0 C13 A:OFH1341 4.8 20.7 1.0 O A:GLY185 4.9 24.1 1.0 O A:HOH2094 4.9 26.2 1.0

Fluorine binding site 2 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:21.2 occ:1.00 F32 A:OFH1341 0.0 21.2 1.0 C8 A:OFH1341 1.3 22.8 1.0 F31 A:OFH1341 2.1 20.1 1.0 F33 A:OFH1341 2.2 26.9 1.0 C1 A:OFH1341 2.4 21.2 1.0 C4 A:OFH1341 2.9 21.3 1.0 O A:HOH2094 3.0 26.2 1.0 O27 A:OFH1341 3.1 21.2 1.0 CA A:GLY191 3.4 21.1 1.0 C A:GLY191 3.4 20.2 1.0 CE A:LYS187 3.4 29.1 1.0 N A:GLY192 3.4 19.9 1.0 C11 A:OFH1341 3.4 22.2 1.0 O A:GLY190 3.5 23.6 1.0 O A:HOH2093 3.7 36.0 1.0 C12 A:OFH1341 3.7 21.9 1.0 N3 A:OFH1341 3.9 21.4 1.0 O A:GLY191 4.0 19.3 1.0 O30 A:OFH1341 4.2 18.9 1.0 C A:GLY190 4.2 24.1 1.0 N A:GLY191 4.2 23.9 1.0 NZ A:LYS187 4.3 30.9 1.0 CA A:GLY192 4.3 19.1 1.0 C9 A:OFH1341 4.5 20.7 1.0 CD A:LYS187 4.6 27.7 1.0 C13 A:OFH1341 4.7 20.7 1.0 CG A:LYS187 4.8 28.2 1.0 O A:HOH2095 4.8 31.0 1.0 C7 A:OFH1341 4.9 19.9 1.0 O A:GLY192 4.9 19.1 1.0 C A:GLY192 5.0 19.1 1.0

Fluorine binding site 3 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:26.9 occ:1.00 F33 A:OFH1341 0.0 26.9 1.0 C8 A:OFH1341 1.3 22.8 1.0 F31 A:OFH1341 2.1 20.1 1.0 F32 A:OFH1341 2.2 21.2 1.0 C1 A:OFH1341 2.3 21.2 1.0 C12 A:OFH1341 2.8 21.9 1.0 C11 A:OFH1341 2.9 22.2 1.0 OH A:TYR193 3.1 24.4 1.0 O A:HOH2097 3.2 29.5 1.0 CE A:LYS187 3.4 29.1 1.0 NZ A:LYS187 3.5 30.9 1.0 CZ A:TYR193 3.6 23.8 1.0 C4 A:OFH1341 3.7 21.3 1.0 CE2 A:TYR193 3.8 24.3 1.0 O A:HOH2093 4.0 36.0 1.0 O27 A:OFH1341 4.4 21.2 1.0 CE1 A:TYR193 4.4 24.5 1.0 N3 A:OFH1341 4.5 21.4 1.0 O A:HOH2094 4.6 26.2 1.0 C9 A:OFH1341 4.6 20.7 1.0 O A:HOH2092 4.7 44.8 1.0 CD A:LYS187 4.8 27.7 1.0 N A:GLY192 4.8 19.9 1.0 O A:HOH2089 4.8 30.4 1.0 CD2 A:TYR193 4.9 22.9 1.0 O A:GLY185 5.0 24.1 1.0

Fluorine binding site 4 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:40.6 occ:1.00 F34 A:OFH1341 0.0 40.6 1.0 C15 A:OFH1341 1.3 40.9 1.0 F35 A:OFH1341 2.1 38.4 1.0 F36 A:OFH1341 2.2 51.9 1.0 C26 A:OFH1341 2.4 36.1 1.0 O28 A:OFH1341 2.7 29.7 1.0 C39 A:OFH1341 3.3 38.6 1.0 OH D:TYR193 3.5 26.4 1.0 C29 A:OFH1341 3.5 27.7 1.0 CE1 A:TYR193 3.7 24.5 1.0 C12 D:OFH1341 3.9 26.9 1.0 OH A:TYR193 3.9 24.4 1.0 F34 D:OFH1341 3.9 41.4 1.0 CZ A:TYR193 4.0 23.8 1.0 O A:HOH2096 4.1 42.0 1.0 C38 D:OFH1341 4.1 28.8 1.0 C38 A:OFH1341 4.2 26.0 1.0 C21 A:OFH1341 4.3 30.2 1.0 CD1 A:TYR193 4.5 24.2 1.0 CZ D:TYR193 4.6 27.0 1.0 O A:HOH2100 4.6 41.3 1.0 C11 D:OFH1341 4.6 28.1 1.0 O28 D:OFH1341 4.7 33.2 1.0 CE1 D:TYR193 4.8 26.0 1.0 C29 D:OFH1341 4.8 32.3 1.0 C20 D:OFH1341 4.8 27.7 1.0

Fluorine binding site 5 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:38.4 occ:1.00 F35 A:OFH1341 0.0 38.4 1.0 C15 A:OFH1341 1.3 40.9 1.0 F34 A:OFH1341 2.1 40.6 1.0 F36 A:OFH1341 2.1 51.9 1.0 C26 A:OFH1341 2.4 36.1 1.0 C39 A:OFH1341 2.6 38.6 1.0 O28 A:OFH1341 3.6 29.7 1.0 C12 D:OFH1341 3.6 26.9 1.0 C11 D:OFH1341 3.7 28.1 1.0 O A:HOH2100 3.8 41.3 1.0 O D:HOH2132 4.2 38.6 1.0 O A:HOH2151 4.2 44.6 1.0 O A:HOH2096 4.5 42.0 1.0 OH D:TYR193 4.6 26.4 1.0 C29 A:OFH1341 4.6 27.7 1.0 CE1 A:TYR193 4.8 24.5 1.0 C1 D:OFH1341 4.8 28.9 1.0 F33 D:OFH1341 4.9 34.0 1.0 O A:HOH2153 5.0 38.4 1.0 C21 A:OFH1341 5.0 30.2 1.0

Fluorine binding site 6 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:51.9 occ:1.00 F36 A:OFH1341 0.0 51.9 1.0 C15 A:OFH1341 1.3 40.9 1.0 F35 A:OFH1341 2.1 38.4 1.0 F34 A:OFH1341 2.2 40.6 1.0 C26 A:OFH1341 2.3 36.1 1.0 CE1 A:TYR193 2.9 24.5 1.0 CD1 A:TYR193 3.1 24.2 1.0 O28 A:OFH1341 3.2 29.7 1.0 O A:HOH2100 3.3 41.3 1.0 C39 A:OFH1341 3.5 38.6 1.0 C29 A:OFH1341 3.5 27.7 1.0 C21 A:OFH1341 3.6 30.2 1.0 CZ A:TYR193 3.6 23.8 1.0 CG A:TYR193 3.9 22.5 1.0 OH A:TYR193 4.2 24.4 1.0 CE2 A:TYR193 4.4 24.3 1.0 O A:HOH2096 4.4 42.0 1.0 CD2 A:TYR193 4.5 22.9 1.0 O A:HOH2153 4.6 38.4 1.0 C38 A:OFH1341 4.6 26.0 1.0 C16 A:OFH1341 4.6 28.0 1.0 O A:HOH2151 4.6 44.6 1.0 CB A:TYR193 4.8 23.0 1.0

Fluorine binding site 7 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F1341 b:23.7 occ:1.00 F31 B:OFH1341 0.0 23.7 1.0 C8 B:OFH1341 1.3 24.1 1.0 F32 B:OFH1341 2.1 24.4 1.0 F33 B:OFH1341 2.2 28.1 1.0 C1 B:OFH1341 2.3 23.5 1.0 C4 B:OFH1341 2.9 23.1 1.0 C9 B:OFH1341 3.0 21.8 1.0 N B:GLY192 3.0 22.6 1.0 N3 B:OFH1341 3.1 21.9 1.0 CA B:GLY192 3.1 22.9 1.0 O B:GLY192 3.1 22.3 1.0 C12 B:OFH1341 3.2 23.6 1.0 C B:GLY192 3.2 20.9 1.0 CE2 B:TYR193 3.3 22.6 1.0 CZ B:TYR193 3.5 22.7 1.0 CD2 B:TYR193 3.6 21.5 1.0 C11 B:OFH1341 3.7 22.8 1.0 C B:GLY191 3.8 23.7 1.0 O27 B:OFH1341 3.8 25.2 1.0 CE1 B:TYR193 3.8 23.1 1.0 OH B:TYR193 4.0 23.1 1.0 CG B:TYR193 4.0 21.5 1.0 N B:TYR193 4.0 22.8 1.0 CD1 B:TYR193 4.1 23.0 1.0 C7 B:OFH1341 4.3 20.7 1.0 O B:GLY191 4.4 21.3 1.0 O30 B:OFH1341 4.4 19.4 1.0 C5 B:OFH1341 4.4 22.4 1.0 CA B:GLY191 4.5 21.2 1.0 NZ B:LYS187 4.5 47.2 1.0 C13 B:OFH1341 4.7 20.1 1.0 CA B:TYR193 4.7 21.5 1.0 C10 B:OFH1341 4.8 22.1 1.0 O B:GLY185 4.9 31.2 1.0 CB B:TYR193 5.0 21.6 1.0

Fluorine binding site 8 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F1341 b:24.4 occ:1.00 F32 B:OFH1341 0.0 24.4 1.0 C8 B:OFH1341 1.3 24.1 1.0 F31 B:OFH1341 2.1 23.7 1.0 F33 B:OFH1341 2.2 28.1 1.0 C1 B:OFH1341 2.2 23.5 1.0 NZ B:LYS187 2.8 47.2 1.0 C4 B:OFH1341 2.8 23.1 1.0 O27 B:OFH1341 3.1 25.2 1.0 C11 B:OFH1341 3.2 22.8 1.0 N B:GLY192 3.2 22.6 1.0 C B:GLY191 3.2 23.7 1.0 CA B:GLY191 3.4 21.2 1.0 C12 B:OFH1341 3.6 23.6 1.0 O B:HOH2062 3.6 42.9 1.0 N3 B:OFH1341 3.8 21.9 1.0 O B:GLY191 3.8 21.3 1.0 O B:GLY190 3.9 24.8 1.0 CE B:LYS187 3.9 43.2 1.0 CA B:GLY192 4.0 22.9 1.0 N B:GLY191 4.3 24.2 1.0 O30 B:OFH1341 4.4 19.4 1.0 C9 B:OFH1341 4.4 21.8 1.0 C B:GLY190 4.5 24.9 1.0 O B:GLY192 4.6 22.3 1.0 C B:GLY192 4.7 20.9 1.0 C13 B:OFH1341 4.8 20.1 1.0 C7 B:OFH1341 4.9 20.7 1.0 CE2 B:TYR193 5.0 22.6 1.0

Fluorine binding site 9 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F1341 b:28.1 occ:1.00 F33 B:OFH1341 0.0 28.1 1.0 C8 B:OFH1341 1.3 24.1 1.0 F32 B:OFH1341 2.2 24.4 1.0 F31 B:OFH1341 2.2 23.7 1.0 C1 B:OFH1341 2.4 23.5 1.0 C12 B:OFH1341 2.8 23.6 1.0 C11 B:OFH1341 2.9 22.8 1.0 OH B:TYR193 3.2 23.1 1.0 NZ B:LYS187 3.5 47.2 1.0 CZ B:TYR193 3.5 22.7 1.0 CE2 B:TYR193 3.5 22.6 1.0 C4 B:OFH1341 3.7 23.1 1.0 CE B:LYS187 3.9 43.2 1.0 O B:HOH2059 4.3 32.8 1.0 CE1 B:TYR193 4.4 23.1 1.0 O27 B:OFH1341 4.5 25.2 1.0 N3 B:OFH1341 4.5 21.9 1.0 CD2 B:TYR193 4.5 21.5 1.0 C9 B:OFH1341 4.6 21.8 1.0 O B:GLY185 4.7 31.2 1.0 N B:GLY192 4.8 22.6 1.0 CA B:GLY192 4.9 22.9 1.0

Fluorine binding site 10 out of 30 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F1341 b:32.6 occ:1.00 F34 B:OFH1341 0.0 32.6 1.0 C15 B:OFH1341 1.3 36.5 1.0 F36 B:OFH1341 2.1 34.2 1.0 F35 B:OFH1341 2.2 39.0 1.0 C26 B:OFH1341 2.3 32.9 1.0 O28 B:OFH1341 2.8 29.2 1.0 C39 B:OFH1341 2.9 30.5 1.0 O B:HOH2061 3.8 38.6 1.0 C29 B:OFH1341 4.1 29.9 1.0 O B:HOH2076 4.8 50.5 1.0 CE1 B:TYR334 4.8 25.8 1.0 C21 B:OFH1341 5.0 30.6 1.0 C38 B:OFH1341 5.0 29.3 1.0

W.Haap, D.W.Banner. Cathepsin S Nitrile Inhibitors To Be Published.