Fluorine in PDB 6ic6: Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1

All present enzymatic activity of Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1:
3.4.14.1;

The structure of Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1, PDB code: 6ic6 was solved by M.Hakansson, D.T.Logan, B.Korkmaz, A.Lesner, M.Wysocka, A.Gieldon, F.Gauthier, D.Jenne, C.Lauritzen, J.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.03 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	86.690, 87.770, 115.030, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 18.6

The structure of Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1 (pdb code 6ic6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1, PDB code: 6ic6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:50.9 occ:1.00 F28 B:H9B403 0.0 50.9 1.0 C25 B:H9B403 1.3 51.0 1.0 F27 B:H9B403 2.2 53.4 1.0 F26 B:H9B403 2.2 55.9 1.0 C20 B:H9B403 2.4 43.5 1.0 C19 B:H9B403 2.8 39.5 1.0 CA A:PRO3 3.4 29.6 1.0 C21 B:H9B403 3.7 39.9 1.0 CB A:PRO3 3.8 30.6 1.0 O A:THR2 4.1 27.1 1.0 N A:PRO3 4.1 27.7 1.0 C18 B:H9B403 4.2 37.5 1.0 O A:HOH347 4.3 40.0 1.0 O A:PRO3 4.3 31.2 1.0 C A:PRO3 4.3 29.6 1.0 C A:THR2 4.4 26.4 1.0 CG A:PRO3 4.6 29.9 1.0 C22 B:H9B403 4.8 37.6 1.0 CD A:PRO3 5.0 29.1 1.0

Fluorine binding site 2 out of 3 in the Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:55.9 occ:1.00 F26 B:H9B403 0.0 55.9 1.0 C25 B:H9B403 1.3 51.0 1.0 F27 B:H9B403 2.2 53.4 1.0 F28 B:H9B403 2.2 50.9 1.0 C20 B:H9B403 2.3 43.5 1.0 C21 B:H9B403 3.2 39.9 1.0 C19 B:H9B403 3.2 39.5 1.0 C22 B:H9B403 4.4 37.6 1.0 C18 B:H9B403 4.5 37.5 1.0 CB A:PRO3 4.5 30.6 1.0 CA A:PRO3 4.6 29.6 1.0 CG A:PRO3 4.8 29.9 1.0 C17 B:H9B403 5.0 35.9 1.0

Fluorine binding site 3 out of 3 in the Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Cathepsin-C in Complex with Cyclopropyl Peptidyl Nitrile Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:53.4 occ:1.00 F27 B:H9B403 0.0 53.4 1.0 C25 B:H9B403 1.3 51.0 1.0 F28 B:H9B403 2.2 50.9 1.0 F26 B:H9B403 2.2 55.9 1.0 C20 B:H9B403 2.3 43.5 1.0 C21 B:H9B403 2.8 39.9 1.0 CA A:PRO3 2.9 29.6 1.0 N A:PRO3 3.0 27.7 1.0 CB A:PRO3 3.2 30.6 1.0 CG A:PRO3 3.2 29.9 1.0 CD A:PRO3 3.4 29.1 1.0 C A:THR2 3.4 26.4 1.0 C19 B:H9B403 3.6 39.5 1.0 O A:THR2 3.7 27.1 1.0 C22 B:H9B403 4.2 37.6 1.0 C A:PRO3 4.4 29.6 1.0 CA A:THR2 4.4 24.1 1.0 O A:ASP1 4.5 23.4 1.0 C18 B:H9B403 4.7 37.5 1.0 O A:HOH341 4.8 40.0 1.0 O A:PRO3 4.9 31.2 1.0 C A:ASP1 5.0 24.0 1.0

B.Korkmaz, A.Lesner, M.Wysocka, A.Gieldon, M.Hakansson, F.Gauthier, D.T.Logan, D.E.Jenne, C.Lauritzen, J.Pedersen. Structure-Based Design and in Vivo Anti-Arthritic Activity Evaluation of A Potent Dipeptidyl Cyclopropyl Nitrile Inhibitor of Cathepsin C. Biochem. Pharmacol. V. 164 349 2019.
ISSN: ISSN 1873-2968
PubMed: 30978322
DOI: 10.1016/J.BCP.2019.04.006