Chlorine in PDB 5qbv: 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: 5qbv 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)	43.28 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.391, 34.311, 104.021, 90.00, 125.27, 90.00
R / Rfree (%)	14.7 / 17.2

The binding sites of Chlorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qbv). 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: 5qbv:
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:22.6 occ:1.00 CL2 A:N2D901 0.0 22.6 1.0 C1 A:N2D901 1.7 15.7 1.0 C2 A:N2D901 2.7 13.3 1.0 C6 A:N2D901 2.7 12.9 1.0 C3 A:N2D901 4.0 11.0 1.0 C5 A:N2D901 4.0 11.0 1.0 CA A:GLY62 4.2 10.6 1.0 O A:HOH1139 4.4 20.6 1.0 C4 A:N2D901 4.5 11.3 1.0 O A:GLY62 4.6 14.1 1.0 CE1 A:PHE70 4.6 12.8 1.0 O A:HOH1238 4.9 23.8 1.0 C A:GLY62 5.0 13.4 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:23.5 occ:1.00 CL3 A:N2D901 0.0 23.5 1.0 C62 A:N2D901 1.7 16.7 1.0 C61 A:N2D901 2.7 19.1 1.0 C63 A:N2D901 2.7 18.2 1.0 C75 A:N2D901 3.0 15.5 1.0 SD A:MET71 3.6 11.5 1.0 N A:GLY165 3.6 9.0 1.0 CA A:GLY165 3.8 7.7 1.0 O A:GLY69 3.9 9.9 1.0 N77 A:N2D901 3.9 15.5 1.0 C64 A:N2D901 4.0 19.8 1.0 C A:HIS164 4.0 10.1 1.0 O A:HOH1211 4.0 20.6 1.0 C60 A:N2D901 4.0 19.2 1.0 CE A:MET71 4.0 10.0 1.0 O A:HIS164 4.4 12.2 1.0 N A:HIS164 4.4 10.4 1.0 CB A:TRP26 4.5 8.6 1.0 C58 A:N2D901 4.5 17.8 1.0 CA A:GLY137 4.5 9.1 1.0 CA A:HIS164 4.6 11.1 1.0 CA A:TRP26 4.9 6.9 1.0 C A:ASN163 4.9 12.1 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:21.6 occ:1.00 CL2 B:N2D901 0.0 21.6 1.0 C1 B:N2D901 1.7 14.7 1.0 C2 B:N2D901 2.7 12.9 1.0 C6 B:N2D901 2.7 14.0 1.0 C3 B:N2D901 3.9 11.2 1.0 C5 B:N2D901 4.0 13.8 1.0 CA B:GLY62 4.1 13.7 1.0 C4 B:N2D901 4.4 12.5 1.0 O B:HOH1203 4.5 20.5 1.0 O B:GLY62 4.6 15.1 1.0 CE1 B:PHE70 4.9 15.3 1.0 C B:GLY62 4.9 14.9 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:23.8 occ:1.00 CL3 B:N2D901 0.0 23.8 1.0 C62 B:N2D901 1.7 18.1 1.0 C61 B:N2D901 2.7 17.2 1.0 C63 B:N2D901 2.7 19.9 1.0 C75 B:N2D901 3.0 18.7 1.0 SD B:MET71 3.6 11.7 1.0 N B:GLY165 3.7 11.4 1.0 O B:GLY69 3.8 11.7 1.0 CA B:GLY165 3.8 9.3 1.0 N77 B:N2D901 3.9 16.4 1.0 O B:HOH1223 3.9 21.3 1.0 C64 B:N2D901 4.0 21.4 1.0 C60 B:N2D901 4.0 20.4 1.0 CE B:MET71 4.0 10.7 1.0 C B:HIS164 4.0 11.4 1.0 O B:HIS164 4.4 11.7 1.0 N B:HIS164 4.5 11.7 1.0 CB B:TRP26 4.5 10.4 1.0 C58 B:N2D901 4.5 19.5 1.0 CA B:HIS164 4.7 9.9 1.0 CA B:GLY137 4.7 10.6 1.0 CA B:TRP26 4.8 9.0 1.0 C B:GLY69 4.9 10.9 1.0 C B:ASN163 4.9 13.1 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