Fluorine in PDB 1vsn: Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K

All present enzymatic activity of Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K:
3.4.22.38;

The structure of Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K, PDB code: 1vsn was solved by M.Mcgrath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.420, 51.000, 104.200, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.9

The binding sites of Fluorine atom in the Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K (pdb code 1vsn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K, PDB code: 1vsn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K within 5.0Å range: probe atom residue distance (Å) B Occ A:F283 b:14.9 occ:1.00 F35 A:NFT283 0.0 14.9 1.0 C16 A:NFT283 1.4 14.5 1.0 F37 A:NFT283 2.2 15.3 1.0 F36 A:NFT283 2.2 15.8 1.0 C15 A:NFT283 2.4 13.7 1.0 C06 A:NFT283 2.9 12.9 1.0 C11 A:NFT283 3.3 12.9 1.0 N24 A:NFT283 3.7 13.2 1.0 C07 A:NFT283 3.7 12.9 1.0 O A:HOH4394 3.8 34.0 1.0 O A:HOH4290 4.1 47.6 1.0 O A:HOH4260 4.1 35.6 1.0 C10 A:NFT283 4.4 12.4 1.0 C17 A:NFT283 4.5 13.4 1.0 C08 A:NFT283 4.7 12.4 1.0 O A:LEU157 5.0 18.0 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K within 5.0Å range: probe atom residue distance (Å) B Occ A:F283 b:15.8 occ:1.00 F36 A:NFT283 0.0 15.8 1.0 C16 A:NFT283 1.4 14.5 1.0 F37 A:NFT283 2.2 15.3 1.0 F35 A:NFT283 2.2 14.9 1.0 C15 A:NFT283 2.4 13.7 1.0 N24 A:NFT283 3.0 13.2 1.0 C06 A:NFT283 3.1 12.9 1.0 C07 A:NFT283 3.3 12.9 1.0 OH A:TYR67 3.4 14.2 1.0 O A:HOH4302 3.6 39.9 1.0 C20 A:NFT283 3.8 14.3 1.0 CZ A:TYR67 3.9 12.3 1.0 CE2 A:TYR67 4.1 12.1 1.0 C17 A:NFT283 4.1 13.4 1.0 C11 A:NFT283 4.3 12.9 1.0 O A:LEU157 4.3 18.0 1.0 C08 A:NFT283 4.5 12.4 1.0 CE1 A:TYR67 4.8 11.7 1.0 C18 A:NFT283 4.8 13.3 1.0 C19 A:NFT283 4.9 14.0 1.0 O A:HOH4390 4.9 44.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of A Potent Small Molecule Inhibitor Bound to Cathepsin K within 5.0Å range: probe atom residue distance (Å) B Occ A:F283 b:15.3 occ:1.00 F37 A:NFT283 0.0 15.3 1.0 C16 A:NFT283 1.4 14.5 1.0 F35 A:NFT283 2.2 14.9 1.0 F36 A:NFT283 2.2 15.8 1.0 C15 A:NFT283 2.5 13.7 1.0 N24 A:NFT283 3.0 13.2 1.0 O A:LEU157 3.2 18.0 1.0 C17 A:NFT283 3.3 13.4 1.0 O A:HOH4260 3.5 35.6 1.0 C20 A:NFT283 3.5 14.3 1.0 O A:HOH4394 3.6 34.0 1.0 CA A:ASN158 3.6 14.9 1.0 C06 A:NFT283 3.7 12.9 1.0 C A:LEU157 4.1 18.4 1.0 C A:ASN158 4.2 13.6 1.0 O A:ASN158 4.3 13.0 1.0 C18 A:NFT283 4.3 13.3 1.0 C22 A:NFT283 4.3 12.0 1.0 N A:ASN158 4.3 16.2 1.0 CB A:ASN158 4.5 14.9 1.0 C19 A:NFT283 4.5 14.0 1.0 C07 A:NFT283 4.6 12.9 1.0 C11 A:NFT283 4.6 12.9 1.0 N26 A:NFT283 4.6 12.1 1.0 O A:HOH4302 4.8 39.9 1.0 O A:HOH4290 4.9 47.6 1.0

C.S.Li, D.Deschenes, S.Desmarais, J.P.Falgueyret, J.Y.Gauthier, D.B.Kimmel, M.E.Mcgrath, D.J.Mckay, M.D.Percival, D.Riendeau, S.B.Rodan, V.L.Truong, G.Wesolowski, R.Zamboni, W.C.Black. Identification of A Potent and Selective Non-Basic Cathepsin K Inhibitor. Bioorg.Med.Chem.Lett. V. 16 1985 2006.
ISSN: ISSN 0960-894X
PubMed: 16413777
DOI: 10.1016/J.BMCL.2005.12.071