Fluorine in PDB 5qby: Crystal Structure of Human Cathepsin-S with Bound Ligand

All present enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand:
3.4.22.27;

The structure of Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qby was solved by S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.87 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.238, 34.376, 103.815, 90.00, 125.10, 90.00
R / Rfree (%)	17.1 / 20.4

The structure of Crystal Structure of Human Cathepsin-S with Bound Ligand also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qby). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qby:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:25.1 occ:1.00 F96 A:N2A901 0.0 25.1 1.0 C87 A:N2A901 1.4 25.2 1.0 C88 A:N2A901 2.3 23.7 1.0 C86 A:N2A901 2.3 26.5 1.0 O A:GLY62 3.1 22.2 1.0 CG A:LYS64 3.3 29.1 1.0 O A:GLY68 3.5 16.5 1.0 CD A:LYS64 3.5 31.7 1.0 N A:LYS64 3.6 23.1 1.0 C89 A:N2A901 3.6 24.1 1.0 C85 A:N2A901 3.6 25.9 1.0 CB A:LYS64 3.7 26.6 1.0 CA A:ASN63 3.8 21.6 1.0 C A:ASN63 3.8 22.4 1.0 C A:GLY68 4.0 17.4 1.0 C A:GLY62 4.0 21.3 1.0 C83 A:N2A901 4.1 24.6 1.0 CA A:LYS64 4.3 24.6 1.0 N A:ASN63 4.3 20.9 1.0 N A:GLY69 4.4 16.5 1.0 CA A:GLY69 4.4 17.2 1.0 O A:ASN63 4.7 21.9 1.0 O A:ASN67 4.7 20.6 1.0 CE A:LYS64 4.8 37.6 1.0 CA A:GLY68 4.8 18.5 1.0 O A:HOH1151 4.9 30.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:26.1 occ:1.00 F96 B:N2A901 0.0 26.1 1.0 C87 B:N2A901 1.4 26.0 1.0 C88 B:N2A901 2.3 25.6 1.0 C86 B:N2A901 2.3 26.0 1.0 O B:GLY62 3.2 22.6 1.0 CD B:LYS64 3.2 34.2 1.0 CG B:LYS64 3.3 30.1 1.0 N B:LYS64 3.6 24.9 1.0 CB B:LYS64 3.6 28.7 1.0 O B:GLY68 3.6 20.3 1.0 C85 B:N2A901 3.6 25.8 1.0 C89 B:N2A901 3.6 26.5 1.0 C B:ASN63 3.8 25.0 1.0 CA B:ASN63 3.8 24.6 1.0 C B:GLY68 4.1 20.6 1.0 C83 B:N2A901 4.1 25.9 1.0 C B:GLY62 4.1 22.6 1.0 CA B:LYS64 4.2 25.9 1.0 CE B:LYS64 4.2 38.9 1.0 N B:ASN63 4.4 23.6 1.0 N B:GLY69 4.5 20.0 1.0 CA B:GLY69 4.6 20.8 1.0 O B:ASN63 4.6 23.2 1.0 O B:ASN67 4.7 22.2 1.0 O B:HOH1101 4.8 26.6 1.0 CA B:GLY68 4.9 20.3 1.0

M.K.Ameriks, S.D.Bembenek, M.T.Burdett, I.C.Choong, J.P.Edwards, D.Gebauer, Y.Gu, L.Karlsson, H.E.Purkey, B.L.Staker, S.Sun, R.L.Thurmond, J.Zhu. Diazinones As P2 Replacements For Pyrazole-Based Cathepsin S Inhibitors Bioorg.Med.Chem.Lett. V. 20 4060 2010.
ISSN: ISSN 0960-894X
PubMed: 20541404
DOI: 10.1016/J.BMCL.2010.05.086