Fluorine in PDB 4bs5: Mouse Cathepsin S with Covalent Ligand

All present enzymatic activity of Mouse Cathepsin S with Covalent Ligand:
3.4.22.27;

The structure of Mouse Cathepsin S with Covalent Ligand, PDB code: 4bs5 was solved by D.W.Banner, J.Benz, B.Gsell, M.Stihle, A.Ruf, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.69 / 1.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.640, 66.790, 54.320, 90.00, 114.06, 90.00
R / Rfree (%)	19.71 / 22.694

The binding sites of Fluorine atom in the Mouse Cathepsin S with Covalent Ligand (pdb code 4bs5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Mouse Cathepsin S with Covalent Ligand, PDB code: 4bs5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:11.4 occ:1.00 F22 A:MG21341 0.0 11.4 1.0 C5 A:MG21341 1.3 10.1 1.0 F20 A:MG21341 2.1 12.5 1.0 F21 A:MG21341 2.1 10.6 1.0 C3 A:MG21341 2.3 7.6 1.0 HB2 A:TYR334 2.6 5.1 1.0 O14 A:MG21341 2.8 7.7 1.0 HE2 A:MET194 2.8 5.6 1.0 HA3 A:GLY260 2.8 3.2 1.0 HB3 A:TYR334 3.0 5.1 1.0 C4 A:MG21341 3.1 7.8 1.0 CB A:TYR334 3.2 5.1 1.0 C23 A:MG21341 3.3 8.8 1.0 HE3 A:MET194 3.4 5.6 1.0 H A:GLY260 3.4 3.5 1.0 S1 A:MG21341 3.5 6.7 1.0 HA A:MG21341 3.5 8.5 1.0 CA A:GLY260 3.5 3.4 1.0 CE A:MET194 3.5 5.9 1.0 N A:GLY260 3.6 3.4 1.0 O A:TYR334 3.8 5.1 1.0 HD1 A:TYR334 3.8 4.5 1.0 HA2 A:GLY260 3.8 3.4 1.0 CG A:TYR334 3.9 5.0 1.0 H25 A:MG21341 3.9 6.2 1.0 HG23 A:VAL285 4.0 6.4 1.0 CD2 A:TYR334 4.1 4.8 1.0 HG22 A:VAL285 4.2 6.7 1.0 HE1 A:MET194 4.2 5.5 1.0 O A:HOH2335 4.2 7.4 1.0 O A:HOH2134 4.2 5.5 1.0 C2 A:MG21341 4.3 6.1 1.0 C A:VAL259 4.4 3.7 1.0 C24 A:MG21341 4.4 8.3 1.0 CA A:TYR334 4.5 4.6 1.0 C25 A:MG21341 4.5 8.4 1.0 C A:TYR334 4.6 4.3 1.0 CG2 A:VAL285 4.6 6.9 1.0 SD A:MET194 4.7 5.5 1.0 HD2 A:TYR193 4.7 6.5 1.0 O15 A:MG21341 4.7 6.4 1.0 C A:GLY260 4.8 3.6 1.0 HA A:VAL259 4.8 3.6 1.0 O A:VAL259 4.8 4.1 1.0 CD1 A:TYR334 4.9 5.2 1.0 HA2 A:GLY288 4.9 3.8 1.0 C26 A:MG21341 5.0 8.8 1.0 O A:HOH2127 5.0 20.9 1.0 O A:HOH2246 5.0 4.4 1.0

Fluorine binding site 2 out of 3 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:12.5 occ:1.00 F20 A:MG21341 0.0 12.5 1.0 C5 A:MG21341 1.3 10.1 1.0 F21 A:MG21341 2.1 10.6 1.0 F22 A:MG21341 2.1 11.4 1.0 C3 A:MG21341 2.3 7.6 1.0 HA A:MG21341 2.4 8.5 1.0 HB3 A:TYR334 2.6 5.1 1.0 C23 A:MG21341 2.7 8.8 1.0 O A:HOH2134 3.0 5.5 1.0 O A:HOH2127 3.1 20.9 1.0 HD2 A:TYR193 3.2 6.5 1.0 O A:HOH2137 3.3 8.1 1.0 CB A:TYR334 3.3 5.1 1.0 HB2 A:TYR334 3.4 5.1 1.0 C4 A:MG21341 3.7 7.8 1.0 O A:HOH2335 3.7 7.4 1.0 CG A:TYR334 3.8 5.0 1.0 HE3 A:MET194 4.0 5.6 1.0 HE2 A:MET194 4.1 5.6 1.0 C25 A:MG21341 4.1 8.4 1.0 CD2 A:TYR193 4.1 6.5 1.0 O A:HOH2218 4.2 14.4 1.0 H25 A:MG21341 4.2 6.2 1.0 HD2 A:TYR334 4.2 5.1 1.0 CD1 A:TYR334 4.3 5.2 1.0 HE2 A:TYR193 4.3 7.2 1.0 O A:TYR334 4.3 5.1 1.0 O14 A:MG21341 4.4 7.7 1.0 CE A:MET194 4.5 5.9 1.0 S1 A:MG21341 4.5 6.7 1.0 CD2 A:TYR334 4.5 4.8 1.0 CA A:TYR334 4.6 4.6 1.0 HB3 A:TYR193 4.7 5.2 1.0 CE2 A:TYR193 4.7 7.1 1.0 HD1 A:TYR334 4.7 4.5 1.0 H A:MET194 4.7 5.2 1.0 HB A:MG21341 4.7 8.6 1.0 C24 A:MG21341 4.7 8.3 1.0 HG22 A:THR195 4.8 5.4 1.0 HA A:TYR334 4.9 4.5 1.0 HA3 A:GLY260 4.9 3.2 1.0 C2 A:MG21341 4.9 6.1 1.0 C A:TYR334 4.9 4.3 1.0 HA A:TYR193 4.9 5.0 1.0 C26 A:MG21341 4.9 8.8 1.0

Fluorine binding site 3 out of 3 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:F1341 b:10.6 occ:1.00 F21 A:MG21341 0.0 10.6 1.0 C5 A:MG21341 1.3 10.1 1.0 F20 A:MG21341 2.1 12.5 1.0 F22 A:MG21341 2.1 11.4 1.0 H25 A:MG21341 2.2 6.2 1.0 C3 A:MG21341 2.4 7.6 1.0 O14 A:MG21341 2.9 7.7 1.0 HE2 A:MET194 2.9 5.6 1.0 C4 A:MG21341 3.0 7.8 1.0 HD2 A:TYR193 3.0 6.5 1.0 C2 A:MG21341 3.0 6.1 1.0 S1 A:MG21341 3.1 6.7 1.0 O A:HOH2134 3.2 5.5 1.0 HE3 A:MET194 3.4 5.6 1.0 CE A:MET194 3.4 5.9 1.0 HA A:TYR193 3.4 5.0 1.0 H A:MET194 3.5 5.2 1.0 C23 A:MG21341 3.6 8.8 1.0 SD A:MET194 3.7 5.5 1.0 CD2 A:TYR193 3.7 6.5 1.0 HA A:MG21341 3.8 8.5 1.0 H16 A:MG21341 4.0 6.0 1.0 C16 A:MG21341 4.1 5.9 1.0 C8 A:MG21341 4.1 5.8 1.0 HE2 A:TYR193 4.2 7.2 1.0 H82C A:MG21341 4.2 5.9 1.0 HB3 A:TYR193 4.2 5.2 1.0 C24 A:MG21341 4.3 8.3 1.0 CA A:TYR193 4.3 4.8 1.0 CE2 A:TYR193 4.3 7.1 1.0 N A:MET194 4.3 5.0 1.0 HE1 A:MET194 4.3 5.5 1.0 H81C A:MG21341 4.4 5.8 1.0 O A:HOH2137 4.4 8.1 1.0 HB3 A:TYR334 4.4 5.1 1.0 H26 A:MG21341 4.4 6.1 1.0 HA3 A:GLY260 4.5 3.2 1.0 CG A:TYR193 4.5 5.9 1.0 O15 A:MG21341 4.5 6.4 1.0 HB2 A:MET194 4.5 5.0 1.0 CB A:TYR193 4.6 5.3 1.0 HB2 A:TYR334 4.6 5.1 1.0 O A:HOH2335 4.6 7.4 1.0 C25 A:MG21341 4.7 8.4 1.0 O A:GLY192 4.8 5.3 1.0 C A:TYR193 4.9 5.5 1.0 CB A:TYR334 4.9 5.1 1.0

H.Hilpert, H.Mauser, R.Humm, L.Anselm, H.Kuehne, G.Hartmann, S.Gruener, D.W.Banner, J.Benz, B.Gsell, A.Kuglstatter, M.Stihle, R.Thoma, R.Alvarez-Sanchez, H.Iding, B.Wirz, W.Haap. Identification of Potent and Selective Cathepsin S (Cats) Inhibitors Containing Different Central Cyclic Scaffolds. J.Med.Chem. V. 56 9789 2013.
ISSN: ISSN 0022-2623
PubMed: 24224654
DOI: 10.1021/JM401528K