Fluorine in PDB 1yt7: Cathepsin K Complexed with A Constrained Ketoamide Inhibitor

All present enzymatic activity of Cathepsin K Complexed with A Constrained Ketoamide Inhibitor:
3.4.22.38;

The structure of Cathepsin K Complexed with A Constrained Ketoamide Inhibitor, PDB code: 1yt7 was solved by D.G.Barrett, V.M.Boncek, J.G.Catalano, D.N.Deaton, A.M.Hassell, C.H.Jurgensen, S.T.Long, R.B.Mcfadyen, A.B.Miller, L.R.Miller, J.A.Payne, J.A.Ray, V.Samano, L.M.Shewchuk, F.X.Tavares, K.J.Wells-Knecht, D.H.Willard, L.L.Wright, H.Q.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 2.30
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	65.645, 65.645, 34.467, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 25.1

The binding sites of Fluorine atom in the Cathepsin K Complexed with A Constrained Ketoamide Inhibitor (pdb code 1yt7). 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 Complexed with A Constrained Ketoamide Inhibitor, PDB code: 1yt7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cathepsin K Complexed with A Constrained Ketoamide 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 Complexed with A Constrained Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:16.3 occ:1.00 F24 A:3FC301 0.0 16.3 1.0 C23 A:3FC301 1.4 13.7 1.0 F25 A:3FC301 2.2 16.4 1.0 F26 A:3FC301 2.2 13.1 1.0 C20 A:3FC301 2.3 13.6 1.0 C21 A:3FC301 2.7 14.9 1.0 CG A:ASP61 3.3 18.4 1.0 CB A:ASP61 3.4 15.6 1.0 OD1 A:ASP61 3.6 18.8 1.0 C19 A:3FC301 3.6 12.1 1.0 OD2 A:ASP61 3.7 16.1 1.0 C22 A:3FC301 4.1 15.2 1.0 CA A:ASP61 4.5 14.4 1.0 C18 A:3FC301 4.7 13.3 1.0 C17 A:3FC301 4.9 15.6 1.0

Fluorine binding site 2 out of 3 in the Cathepsin K Complexed with A Constrained Ketoamide 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 Complexed with A Constrained Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:16.4 occ:1.00 F25 A:3FC301 0.0 16.4 1.0 C23 A:3FC301 1.4 13.7 1.0 F26 A:3FC301 2.2 13.1 1.0 F24 A:3FC301 2.2 16.3 1.0 C20 A:3FC301 2.3 13.6 1.0 C19 A:3FC301 3.0 12.1 1.0 C21 A:3FC301 3.3 14.9 1.0 C18 A:3FC301 4.3 13.3 1.0 C22 A:3FC301 4.5 15.2 1.0 C17 A:3FC301 4.9 15.6 1.0

Fluorine binding site 3 out of 3 in the Cathepsin K Complexed with A Constrained Ketoamide 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 Complexed with A Constrained Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:13.1 occ:1.00 F26 A:3FC301 0.0 13.1 1.0 C23 A:3FC301 1.4 13.7 1.0 F25 A:3FC301 2.2 16.4 1.0 F24 A:3FC301 2.2 16.3 1.0 C20 A:3FC301 2.3 13.6 1.0 C19 A:3FC301 2.8 12.1 1.0 CB A:ASP61 3.5 15.6 1.0 C21 A:3FC301 3.5 14.9 1.0 O A:ASN60 3.7 13.0 1.0 C A:ASN60 3.7 12.9 1.0 N A:ASP61 3.8 13.8 1.0 O A:GLU59 3.9 15.3 1.0 CA A:ASP61 4.0 14.4 1.0 CG A:ASP61 4.1 18.4 1.0 C18 A:3FC301 4.1 13.3 1.0 OD1 A:ASP61 4.2 18.8 1.0 CA A:ASN60 4.4 13.8 1.0 C A:GLU59 4.6 15.3 1.0 C22 A:3FC301 4.7 15.2 1.0 N A:ASN60 4.9 13.8 1.0 C17 A:3FC301 4.9 15.6 1.0 OD2 A:ASP61 4.9 16.1 1.0

D.G.Barrett, V.M.Boncek, J.G.Catalano, D.N.Deaton, A.M.Hassell, C.H.Jurgensen, S.T.Long, R.B.Mcfadyen, A.B.Miller, L.R.Miller, J.A.Payne, J.A.Ray, V.Samano, L.M.Shewchuk, F.X.Tavares, K.J.Wells-Knecht, D.H.Willard, L.L.Wright, H.Q.Zhou. P(2)-P(3) Conformationally Constrained Ketoamide-Based Inhibitors of Cathepsin K. Bioorg.Med.Chem.Lett. V. 15 3540 2005.
ISSN: ISSN 0960-894X
PubMed: 15982880
DOI: 10.1016/J.BMCL.2005.05.062