Fluorine in PDB 3ovz: Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead

All present enzymatic activity of Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead:
3.4.22.38;

The structure of Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead, PDB code: 3ovz was solved by X.Fradera, M.Van Zeeland, J.C.M.Uitdehaag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.16 / 2.02
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.741, 55.741, 128.916, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 30.8

The structure of Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead (pdb code 3ovz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead, PDB code: 3ovz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:38.7 occ:1.00 F21 A:O961 0.0 38.7 1.0 C20 A:O961 1.4 34.6 1.0 F23 A:O961 2.1 38.8 1.0 F22 A:O961 2.1 39.6 1.0 C17 A:O961 2.5 32.7 1.0 C18 A:O961 3.2 33.2 1.0 CL19 A:O961 3.3 34.2 1.0 C16 A:O961 3.5 33.0 1.0 CD2 A:TYR67 3.6 28.4 1.0 O24 A:O961 3.6 31.9 1.0 CB A:ALA134 3.7 30.8 1.0 CD2 A:LEU209 3.8 31.9 1.0 CE2 A:TYR67 3.9 27.8 1.0 SD A:MET68 4.0 34.2 1.0 CE A:MET68 4.1 30.6 1.0 O A:GLY66 4.3 30.9 1.0 C11 A:O961 4.6 31.9 1.0 CG A:TYR67 4.7 29.6 1.0 CA A:TYR67 4.7 30.6 1.0 C14 A:O961 4.8 33.7 1.0 CG A:LEU209 4.8 33.3 1.0 O A:HOH269 4.8 30.9 1.0 CA A:ALA134 4.8 30.6 1.0 C36 A:O961 4.9 36.1 1.0 C25 A:O961 5.0 35.7 1.0 CB A:TYR67 5.0 30.1 1.0

Fluorine binding site 2 out of 3 in the Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:39.6 occ:1.00 F22 A:O961 0.0 39.6 1.0 C20 A:O961 1.3 34.6 1.0 F21 A:O961 2.1 38.7 1.0 F23 A:O961 2.1 38.8 1.0 C17 A:O961 2.3 32.7 1.0 CL19 A:O961 2.9 34.2 1.0 C18 A:O961 2.9 33.2 1.0 CB A:ALA134 3.1 30.8 1.0 C16 A:O961 3.4 33.0 1.0 O A:HIS162 3.4 27.6 1.0 N A:HIS162 3.4 28.5 1.0 C A:HIS162 3.6 27.7 1.0 O24 A:O961 3.7 31.9 1.0 CA A:ALA134 3.8 30.6 1.0 C A:ASN161 4.0 29.7 1.0 CA A:HIS162 4.0 28.0 1.0 N A:ALA163 4.1 27.6 1.0 C11 A:O961 4.2 31.9 1.0 N A:ASN161 4.3 32.8 1.0 CA A:ASN161 4.4 31.5 1.0 C A:LEU160 4.5 34.1 1.0 CA A:ALA163 4.5 27.6 1.0 O A:ASN161 4.5 29.8 1.0 CB A:LEU160 4.6 35.6 1.0 CB A:ALA163 4.6 27.3 1.0 C14 A:O961 4.6 33.7 1.0 C A:ALA134 4.7 31.2 1.0 N A:ILE135 4.7 31.9 1.0 O A:LEU160 4.7 34.5 1.0 O A:ILE135 4.9 31.4 1.0 C12 A:O961 4.9 34.0 1.0 N A:ALA134 4.9 29.6 1.0

Fluorine binding site 3 out of 3 in the Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin K in Complex with A Covalent Inhibitor with A Ketoamide Warhead within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:38.8 occ:1.00 F23 A:O961 0.0 38.8 1.0 C20 A:O961 1.4 34.6 1.0 F21 A:O961 2.1 38.7 1.0 F22 A:O961 2.1 39.6 1.0 O24 A:O961 2.3 31.9 1.0 C17 A:O961 2.4 32.7 1.0 C16 A:O961 2.8 33.0 1.0 C36 A:O961 3.3 36.1 1.0 CB A:ALA134 3.5 30.8 1.0 CB A:LEU160 3.5 35.6 1.0 C25 A:O961 3.5 35.7 1.0 CD2 A:LEU209 3.6 31.9 1.0 C18 A:O961 3.7 33.2 1.0 C28 A:O961 3.9 35.7 1.0 O A:LEU160 3.9 34.5 1.0 C A:LEU160 4.1 34.1 1.0 CE2 A:TYR67 4.2 27.8 1.0 C14 A:O961 4.2 33.7 1.0 CL19 A:O961 4.4 34.2 1.0 C34 A:O961 4.4 37.1 1.0 CA A:LEU160 4.4 35.6 1.0 CD1 A:LEU160 4.4 32.9 1.0 CD2 A:TYR67 4.5 28.4 1.0 N A:ASN161 4.5 32.8 1.0 CG A:LEU160 4.6 34.5 1.0 CA A:ALA134 4.8 30.6 1.0 CG A:LEU209 4.8 33.3 1.0 CA A:ASN161 4.9 31.5 1.0 CB A:LEU209 4.9 32.2 1.0 C11 A:O961 4.9 31.9 1.0 N A:HIS162 4.9 28.5 1.0

J.Cai, J.Robinson, S.Belshaw, K.Everett, X.Fradera, M.Van Zeeland, L.Van Berkom, P.Van Rijnsbergen, L.Popplestone, M.Baugh, M.Dempster, J.Bruin, W.Hamilton, E.Kinghorn, P.Westwood, J.Kerr, Z.Rankovic, W.Arbuckle, D.J.Bennett, P.S.Jones, C.Long, I.Martin, J.C.Uitdehaag, T.Meulemans. Trifluoromethylphenyl As P2 For Ketoamide-Based Cathepsin S Inhibitors. Bioorg.Med.Chem.Lett. V. 20 6890 2010.
ISSN: ISSN 0960-894X
PubMed: 21030256
DOI: 10.1016/J.BMCL.2010.10.012