Fluorine in PDB 3kwz: Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor

All present enzymatic activity of Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor:
3.4.22.38;

The structure of Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor, PDB code: 3kwz was solved by X.Fradera, J.C.M.Uitdehaag, M.Van Zeeland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.22 / 1.49
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.814, 55.814, 129.115, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 29.9

The binding sites of Fluorine atom in the Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor (pdb code 3kwz). 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 Non-Selective 2-Cyano-Pyrimidine Inhibitor, PDB code: 3kwz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor


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 Non-Selective 2-Cyano-Pyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F222 b:33.4 occ:1.00 F18 A:KWZ222 0.0 33.4 1.0 C17 A:KWZ222 1.3 30.6 1.0 F19 A:KWZ222 2.1 33.0 1.0 F20 A:KWZ222 2.2 34.6 1.0 C13 A:KWZ222 2.3 29.9 1.0 C12 A:KWZ222 2.9 29.6 1.0 O A:HIS162 3.1 18.3 1.0 C A:HIS162 3.1 19.7 1.0 CB A:ALA134 3.2 21.1 1.0 N A:ALA163 3.4 19.0 1.0 C14 A:KWZ222 3.5 28.6 1.0 N A:HIS162 3.6 21.0 1.0 CA A:ALA163 3.7 19.3 1.0 CB A:ALA163 3.7 18.3 1.0 CA A:ALA134 3.8 20.9 1.0 CA A:HIS162 3.8 20.5 1.0 C7 A:KWZ222 4.3 28.6 1.0 C A:ASN161 4.4 21.3 1.0 C15 A:KWZ222 4.6 29.8 1.0 SD A:MET68 4.7 25.7 1.0 N A:ILE135 4.7 22.5 1.0 N A:ASN161 4.7 23.4 1.0 C A:ALA134 4.7 21.6 1.0 O A:GLY66 4.8 19.9 1.0 N A:ALA134 4.9 21.2 1.0 CE A:MET68 4.9 21.7 1.0 CA A:ASN161 4.9 22.7 1.0 C A:LEU160 5.0 24.6 1.0 C16 A:KWZ222 5.0 29.3 1.0

Fluorine binding site 2 out of 3 in the Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor


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 Non-Selective 2-Cyano-Pyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F222 b:33.0 occ:1.00 F19 A:KWZ222 0.0 33.0 1.0 C17 A:KWZ222 1.3 30.6 1.0 F20 A:KWZ222 2.1 34.6 1.0 F18 A:KWZ222 2.1 33.4 1.0 C13 A:KWZ222 2.3 29.9 1.0 C14 A:KWZ222 2.6 28.6 1.0 CB A:ALA134 3.3 21.1 1.0 CD2 A:LEU209 3.5 26.3 1.0 C12 A:KWZ222 3.6 29.6 1.0 CE2 A:TYR67 3.8 27.9 1.0 CD2 A:TYR67 3.9 25.4 1.0 C15 A:KWZ222 4.0 29.8 1.0 CB A:LEU160 4.4 25.4 1.0 O A:LEU160 4.6 24.7 1.0 CA A:ALA134 4.6 20.9 1.0 C7 A:KWZ222 4.7 28.6 1.0 C A:LEU160 4.7 24.6 1.0 O A:GLY66 4.7 19.9 1.0 CG A:LEU209 4.8 25.6 1.0 C16 A:KWZ222 4.9 29.3 1.0 O A:HIS162 5.0 18.3 1.0

Fluorine binding site 3 out of 3 in the Cathepsin K in Complex with A Non-Selective 2-Cyano-Pyrimidine Inhibitor


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 Non-Selective 2-Cyano-Pyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F222 b:34.6 occ:1.00 F20 A:KWZ222 0.0 34.6 1.0 C17 A:KWZ222 1.3 30.6 1.0 F19 A:KWZ222 2.1 33.0 1.0 F18 A:KWZ222 2.2 33.4 1.0 C13 A:KWZ222 2.4 29.9 1.0 O A:GLY66 3.0 19.9 1.0 C12 A:KWZ222 3.1 29.6 1.0 C14 A:KWZ222 3.4 28.6 1.0 SD A:MET68 3.6 25.7 1.0 CD2 A:TYR67 3.7 25.4 1.0 CA A:TYR67 4.1 22.8 1.0 C A:GLY66 4.1 21.4 1.0 CB A:ALA163 4.1 18.3 1.0 CE2 A:TYR67 4.2 27.9 1.0 CB A:ALA134 4.3 21.1 1.0 C7 A:KWZ222 4.4 28.6 1.0 CE A:MET68 4.4 21.7 1.0 N A:TYR67 4.5 22.8 1.0 CD2 A:LEU209 4.6 26.3 1.0 CG A:TYR67 4.6 23.9 1.0 C15 A:KWZ222 4.6 29.8 1.0 CA A:ALA163 4.8 19.3 1.0 N A:MET68 4.8 22.4 1.0 N A:ALA163 4.8 19.0 1.0 CB A:TYR67 4.8 23.6 1.0 CB A:TRP26 4.8 20.1 1.0 O A:HOH363 5.0 23.6 1.0 C A:TYR67 5.0 21.9 1.0

Z.Rankovic, J.Cai, J.Kerr, X.Fradera, J.Robinson, A.Mistry, E.Hamilton, G.Mcgarry, F.Andrews, W.Caulfield, I.Cumming, M.Dempster, J.Waller, P.Scullion, I.Martin, A.Mitchell, C.Long, M.Baugh, P.Westwood, E.Kinghorn, J.Bruin, W.Hamilton, J.Uitdehaag, M.Van Zeeland, D.Potin, L.Saniere, A.Fouquet, F.Chevallier, H.Deronzier, C.Dorleans, E.Nicolai. Design and Optimization of A Series of Novel 2-Cyano-Pyrimidines As Cathepsin K Inhibitors Bioorg.Med.Chem.Lett. V. 20 1524 2010.
ISSN: ISSN 0960-894X
PubMed: 20149657
DOI: 10.1016/J.BMCL.2010.01.100