Fluorine in PDB 4dmy: Cathepsin K Inhibitor

All present enzymatic activity of Cathepsin K Inhibitor:
3.4.22.38;

The structure of Cathepsin K Inhibitor, PDB code: 4dmy was solved by A.G.Dossetter, H.Beeley, J.Bowyer, C.R.Cook, J.J.Crawford, J.E.Finlayson, N.M.Heron, C.Heyes, A.J.Highton, J.A.Hudson, P.W.Kenny, S.Martin, P.A.Macfaul, T.M.Mcguire, P.M.Gutierrez, A.D.Morley, J.J.Morris, K.M.Page, L.Rosenbrier Ribeiro, H.Sawney, S.Steinbacher, S.Krapp, A.Jestel, C.Smith, M.Vickers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.88 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.927, 69.554, 90.645, 90.00, 99.83, 90.00
R / Rfree (%)	12.8 / 19

The binding sites of Fluorine atom in the Cathepsin K Inhibitor (pdb code 4dmy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Cathepsin K Inhibitor, PDB code: 4dmy:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Cathepsin K 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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:21.6 occ:1.00 F14 A:0LC301 0.0 21.6 1.0 C6 A:0LC301 1.3 23.9 1.0 C8 A:0LC301 2.4 22.7 1.0 C7 A:0LC301 2.4 19.9 1.0 OD1 A:ASN60 3.1 16.0 1.0 ND2 A:ASN70 3.2 8.6 1.0 CD2 A:TYR67 3.3 15.5 1.0 C5 A:0LC301 3.6 19.7 1.0 C9 A:0LC301 3.7 22.6 1.0 CE2 A:TYR67 3.7 20.8 1.0 O A:GLU59 4.0 24.8 1.0 C4 A:0LC301 4.1 22.0 1.0 O A:HOH456 4.1 28.2 1.0 N A:TYR67 4.2 14.5 1.0 CG A:TYR67 4.2 17.2 1.0 CG A:ASN60 4.2 15.9 1.0 CA A:ASN60 4.3 18.1 1.0 CA A:GLY66 4.5 15.8 1.0 CG A:ASN70 4.6 8.5 1.0 C A:GLU59 4.6 23.7 1.0 CB A:TYR67 4.6 14.6 1.0 N A:ASN60 4.6 21.2 1.0 C A:GLY66 4.7 15.0 1.0 CB A:ASN60 4.8 17.1 1.0 C2 A:0LC301 4.9 20.7 1.0 CZ A:TYR67 4.9 19.2 1.0

Fluorine binding site 2 out of 2 in the Cathepsin K 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 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:26.8 occ:1.00 F14 B:0LC301 0.0 26.8 1.0 C6 B:0LC301 1.3 30.6 1.0 C8 B:0LC301 2.4 32.2 1.0 C7 B:0LC301 2.4 31.7 1.0 ND2 B:ASN70 3.0 13.1 1.0 O B:GLU59 3.1 19.2 1.0 OD1 B:ASN60 3.2 15.2 1.0 CD2 B:TYR67 3.3 16.6 1.0 C5 B:0LC301 3.6 31.4 1.0 C9 B:0LC301 3.6 33.2 1.0 CE2 B:TYR67 3.9 22.1 1.0 C4 B:0LC301 4.1 31.7 1.0 C B:GLU59 4.2 17.7 1.0 CG B:TYR67 4.3 16.9 1.0 CG B:ASN70 4.3 12.2 1.0 N B:TYR67 4.3 13.0 1.0 CA B:ASN60 4.4 15.4 1.0 CG B:ASN60 4.4 11.1 1.0 CB B:TYR67 4.5 13.2 1.0 CA B:GLY66 4.7 15.0 1.0 N B:ASN60 4.7 14.2 1.0 C B:GLY66 4.9 10.7 1.0 C2 B:0LC301 4.9 30.8 1.0 CB B:ASN60 5.0 15.7 1.0

A.G.Dossetter, H.Beeley, J.Bowyer, C.R.Cook, J.J.Crawford, J.E.Finlayson, N.M.Heron, C.Heyes, A.J.Highton, J.A.Hudson, A.Jestel, P.W.Kenny, S.Krapp, S.Martin, P.A.Macfaul, T.M.Mcguire, P.M.Gutierrez, A.D.Morley, J.J.Morris, K.M.Page, L.R.Ribeiro, H.Sawney, S.Steinbacher, C.Smith, M.Vickers. (1R,2R)-N-(1-Cyanocyclopropyl)-2-(6-Methoxy-1,3,4, 5-Tetrahydropyrido[4,3-B]Indole-2-Carbonyl) Cyclohexanecarboxamide (AZD4996): A Potent and Highly Selective Cathepsin K Inhibitor For the Treatment of Osteoarthritis. J.Med.Chem. V. 55 6363 2012.
ISSN: ISSN 0022-2623
PubMed: 22742641
DOI: 10.1021/JM3007257