Fluorine in PDB 3kw9: X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand

All present enzymatic activity of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand:
3.4.22.38;

The structure of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand, PDB code: 3kw9 was solved by 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)	50.00 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.391, 55.391, 128.719, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 25.9

The binding sites of Fluorine atom in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand (pdb code 3kw9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand, PDB code: 3kw9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F217 b:42.2 occ:1.00 F1 A:TFA217 0.0 42.2 1.0 C2 A:TFA217 1.2 43.7 1.0 F2 A:TFA217 1.9 45.5 1.0 F3 A:TFA217 2.0 43.0 1.0 C1 A:TFA217 2.2 45.6 1.0 O A:TFA217 2.5 48.2 1.0 O A:HOH287 2.9 53.5 1.0 N15 A:ORG216 3.2 25.1 1.0 NE2 A:GLN19 3.3 24.7 1.0 OXT A:TFA217 3.4 46.4 1.0 NE1 A:TRP184 3.4 16.1 1.0 ND1 A:HIS162 3.4 22.9 1.0 CE1 A:HIS162 3.4 21.4 1.0 CZ2 A:TRP184 3.8 18.1 1.0 CE2 A:TRP184 3.9 18.0 1.0 C9 A:ORG216 4.1 24.3 1.0 CD A:GLN19 4.1 23.7 1.0 OE1 A:GLN19 4.4 22.3 1.0 CD1 A:TRP184 4.6 17.8 1.0 NE2 A:HIS162 4.6 21.3 1.0 CG A:HIS162 4.6 22.6 1.0 N5 A:ORG216 4.7 25.5 1.0 C6 A:ORG216 4.8 26.2 1.0

Fluorine binding site 2 out of 3 in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F217 b:45.5 occ:1.00 F2 A:TFA217 0.0 45.5 1.0 C2 A:TFA217 1.2 43.7 1.0 F1 A:TFA217 1.9 42.2 1.0 F3 A:TFA217 1.9 43.0 1.0 C1 A:TFA217 2.2 45.6 1.0 OXT A:TFA217 2.7 46.4 1.0 O A:TFA217 3.2 48.2 1.0 NE2 A:GLN19 3.3 24.7 1.0 NE1 A:TRP184 3.8 16.1 1.0 CD A:GLN19 4.3 23.7 1.0 N15 A:ORG216 4.4 25.1 1.0 CE2 A:TRP184 4.5 18.0 1.0 CZ2 A:TRP184 4.7 18.1 1.0 CD1 A:TRP184 4.7 17.8 1.0 O A:HOH287 4.7 53.5 1.0 O A:GLY20 4.9 29.6 1.0 O A:CYS22 5.0 24.7 1.0

Fluorine binding site 3 out of 3 in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F217 b:43.0 occ:1.00 F3 A:TFA217 0.0 43.0 1.0 C2 A:TFA217 1.2 43.7 1.0 F2 A:TFA217 1.9 45.5 1.0 F1 A:TFA217 2.0 42.2 1.0 C1 A:TFA217 2.1 45.6 1.0 OXT A:TFA217 2.7 46.4 1.0 N15 A:ORG216 3.1 25.1 1.0 O A:TFA217 3.1 48.2 1.0 NE2 A:GLN19 3.3 24.7 1.0 CA A:GLY23 3.8 24.9 1.0 N5 A:ORG216 3.8 25.5 1.0 O A:HOH287 3.8 53.5 1.0 C14 A:ORG216 3.9 32.5 1.0 C9 A:ORG216 4.0 24.3 1.0 C13 A:ORG216 4.2 33.8 1.0 C6 A:ORG216 4.3 26.2 1.0 O A:CYS22 4.5 24.7 1.0 CD A:GLN19 4.5 23.7 1.0 N A:GLY23 4.6 25.4 1.0 C A:GLY23 4.8 23.1 1.0 C4 A:ORG216 4.8 28.3 1.0 N8 A:ORG216 4.9 31.8 1.0 C A:CYS22 4.9 26.5 1.0 ND1 A:HIS162 5.0 22.9 1.0 NE1 A:TRP184 5.0 16.1 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