Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qby:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl901 b:33.7 occ:1.00 CL24 A:N2A901 0.0 33.7 1.0 C1 A:N2A901 1.7 26.1 1.0 C2 A:N2A901 2.7 25.6 1.0 C6 A:N2A901 2.7 24.5 1.0 C3 A:N2A901 4.0 23.9 1.0 C5 A:N2A901 4.0 23.6 1.0 C4 A:N2A901 4.5 24.1 1.0 CA A:GLY62 4.6 21.5 1.0 O A:GLY62 4.8 22.2 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl901 b:33.2 occ:1.00 CL73 A:N2A901 0.0 33.2 1.0 C64 A:N2A901 1.7 27.0 1.0 C63 A:N2A901 2.7 27.4 1.0 C65 A:N2A901 2.7 25.6 1.0 C75 A:N2A901 3.0 24.5 1.0 N A:GLY165 3.3 16.8 1.0 C A:HIS164 3.6 17.2 1.0 CA A:GLY165 3.6 17.5 1.0 O A:HOH1146 3.7 21.0 1.0 N77 A:N2A901 3.9 23.5 1.0 SD A:MET71 3.9 18.9 1.0 C62 A:N2A901 4.0 28.5 1.0 N A:HIS164 4.0 19.2 1.0 C66 A:N2A901 4.0 28.0 1.0 O A:HIS164 4.0 16.8 1.0 O A:GLY69 4.1 18.8 1.0 CA A:HIS164 4.1 18.1 1.0 C A:ASN163 4.4 21.0 1.0 C60 A:N2A901 4.5 28.3 1.0 CA A:GLY137 4.5 17.8 1.0 CE A:MET71 4.6 19.0 1.0 CB A:TRP26 4.6 18.6 1.0 OG A:SER25 4.8 16.0 1.0 O A:ASN163 4.8 20.9 1.0 O A:HOH1075 4.8 27.4 1.0 CA A:TRP26 4.9 18.7 1.0 CG2 A:VAL162 5.0 20.9 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:29.3 occ:1.00 CL24 B:N2A901 0.0 29.3 1.0 C1 B:N2A901 1.7 25.0 1.0 C2 B:N2A901 2.7 24.0 1.0 C6 B:N2A901 2.7 24.3 1.0 C3 B:N2A901 4.0 23.9 1.0 C5 B:N2A901 4.0 23.7 1.0 CA B:GLY62 4.4 21.8 1.0 C4 B:N2A901 4.5 23.6 1.0 O B:GLY62 4.7 22.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:30.3 occ:1.00 CL73 B:N2A901 0.0 30.3 1.0 C64 B:N2A901 1.8 29.1 1.0 C63 B:N2A901 2.7 29.1 1.0 C65 B:N2A901 2.7 27.2 1.0 C75 B:N2A901 3.1 26.9 1.0 N B:GLY165 3.2 18.9 1.0 C B:HIS164 3.5 18.6 1.0 CA B:GLY165 3.6 18.3 1.0 O B:HOH1117 3.8 23.5 1.0 N B:HIS164 3.8 21.5 1.0 N77 B:N2A901 4.0 27.8 1.0 CA B:HIS164 4.0 19.9 1.0 O B:HIS164 4.0 18.4 1.0 C62 B:N2A901 4.0 29.6 1.0 C66 B:N2A901 4.0 28.7 1.0 SD B:MET71 4.1 18.0 1.0 O B:GLY69 4.1 21.6 1.0 C B:ASN163 4.3 21.0 1.0 C60 B:N2A901 4.5 29.4 1.0 CB B:TRP26 4.5 19.5 1.0 OG B:SER25 4.5 16.0 1.0 O B:ASN163 4.6 23.2 1.0 CA B:GLY137 4.7 19.5 1.0 CE B:MET71 4.8 19.2 1.0 CA B:TRP26 4.9 19.0 1.0 O B:HOH1142 4.9 41.7 1.0 CA B:ASN163 5.0 21.7 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