Fluorine in PDB 6ex8: Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor

The structure of Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor, PDB code: 6ex8 was solved by U.Dietzel, C.Kisker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.03 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	31.830, 49.753, 67.569, 103.56, 98.89, 100.81
R / Rfree (%)	13.6 / 17.7

The structure of Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor (pdb code 6ex8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor, PDB code: 6ex8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor


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 Rhodesain in Complex with A Macrolactam Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:32.9 occ:1.00 FAE A:C2K301 0.0 32.9 1.0 CBI A:C2K301 1.4 33.9 1.0 FAF A:C2K301 2.2 40.0 1.0 FAD A:C2K301 2.3 31.0 1.0 CBD A:C2K301 2.3 31.1 1.0 CAJ A:C2K301 3.0 27.1 1.0 CAN A:C2K301 3.3 28.1 1.0 CE2 A:PHE61 3.6 24.1 1.0 CD2 A:PHE61 4.3 24.1 1.0 CAL A:C2K301 4.3 26.2 1.0 CZ A:PHE61 4.3 25.5 1.0 CBF A:C2K301 4.5 29.9 1.0 O A:HOH550 4.9 39.8 1.0 CBG A:C2K301 4.9 25.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor


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 Rhodesain in Complex with A Macrolactam Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:40.0 occ:1.00 FAF A:C2K301 0.0 40.0 1.0 CBI A:C2K301 1.3 33.9 1.0 FAD A:C2K301 2.1 31.0 1.0 FAE A:C2K301 2.2 32.9 1.0 CBD A:C2K301 2.2 31.1 1.0 CAN A:C2K301 2.6 28.1 1.0 CAJ A:C2K301 3.5 27.1 1.0 CD1 A:LEU67 3.6 22.5 1.0 CBF A:C2K301 4.0 29.9 1.0 CG A:LEU67 4.2 20.8 1.0 ND2 A:ASN70 4.3 24.4 1.0 CAL A:C2K301 4.6 26.2 1.0 CAR A:C2K301 4.8 29.5 1.0 CBG A:C2K301 4.9 25.7 1.0 OAY A:C2K301 5.0 31.0 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor


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 Rhodesain in Complex with A Macrolactam Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:31.0 occ:1.00 FAD A:C2K301 0.0 31.0 1.0 CBI A:C2K301 1.4 33.9 1.0 FAF A:C2K301 2.1 40.0 1.0 FAE A:C2K301 2.3 32.9 1.0 CBD A:C2K301 2.3 31.1 1.0 CAJ A:C2K301 2.8 27.1 1.0 ND2 A:ASN70 3.2 24.4 1.0 CAN A:C2K301 3.5 28.1 1.0 CE2 A:PHE61 3.6 24.1 1.0 CD2 A:PHE61 4.1 24.1 1.0 OD1 A:ASP60 4.2 18.3 1.0 CAL A:C2K301 4.2 26.2 1.0 CD1 A:LEU67 4.2 22.5 1.0 CG A:LEU67 4.3 20.8 1.0 CG A:ASN70 4.5 23.3 1.0 CBF A:C2K301 4.7 29.9 1.0 CZ A:PHE61 4.7 25.5 1.0 O A:ILE59 4.7 20.8 1.0 CA A:GLY66 4.9 17.8 1.0 N A:LEU67 4.9 16.9 1.0 CBG A:C2K301 5.0 25.7 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F305 b:41.1 occ:1.00 FAE B:C2K305 0.0 41.1 1.0 CBI B:C2K305 1.3 44.2 1.0 FAD B:C2K305 2.2 48.8 1.0 CBD B:C2K305 2.3 40.3 1.0 FAF B:C2K305 2.4 51.6 1.0 CAJ B:C2K305 2.9 34.9 1.0 CE1 B:PHE61 3.3 25.4 1.0 CAN B:C2K305 3.4 38.0 1.0 CZ B:PHE61 3.9 26.1 1.0 CD1 B:PHE61 4.1 23.7 1.0 O B:HOH401 4.2 42.1 1.0 CAL B:C2K305 4.2 36.0 1.0 CBF B:C2K305 4.6 39.3 1.0 CBG B:C2K305 5.0 32.2 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F305 b:51.6 occ:1.00 FAF B:C2K305 0.0 51.6 1.0 CBI B:C2K305 1.6 44.2 1.0 FAD B:C2K305 2.4 48.8 1.0 FAE B:C2K305 2.4 41.1 1.0 CBD B:C2K305 2.5 40.3 1.0 CAN B:C2K305 2.8 38.0 1.0 CAJ B:C2K305 3.8 34.9 1.0 CD1 B:LEU67 4.2 27.2 1.0 CBF B:C2K305 4.2 39.3 1.0 O B:HOH401 4.7 42.1 1.0 CG B:LEU67 4.7 22.7 1.0 CAL B:C2K305 4.9 36.0 1.0 ND2 B:ASN70 5.0 30.5 1.0 CAR B:C2K305 5.0 39.7 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Rhodesain in Complex with A Macrolactam Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F305 b:48.8 occ:1.00 FAD B:C2K305 0.0 48.8 1.0 CBI B:C2K305 1.4 44.2 1.0 FAE B:C2K305 2.2 41.1 1.0 CBD B:C2K305 2.3 40.3 1.0 FAF B:C2K305 2.4 51.6 1.0 O B:HOH401 2.4 42.1 1.0 CAJ B:C2K305 2.9 34.9 1.0 ND2 B:ASN70 3.3 30.5 1.0 CAN B:C2K305 3.4 38.0 1.0 CE1 B:PHE61 3.8 25.4 1.0 CG B:LEU67 4.1 22.7 1.0 CD1 B:LEU67 4.1 27.2 1.0 CAL B:C2K305 4.2 36.0 1.0 CD1 B:PHE61 4.5 23.7 1.0 OD1 B:ASP60 4.5 17.7 1.0 CG B:ASN70 4.6 26.6 1.0 CBF B:C2K305 4.6 39.3 1.0 O B:ILE59 4.8 21.7 1.0 CZ B:PHE61 4.8 26.1 1.0 CB B:LEU67 4.9 20.2 1.0 CBG B:C2K305 4.9 32.2 1.0

M.Giroud, U.Dietzel, L.Anselm, D.Banner, A.Kuglstatter, J.Benz, J.B.Blanc, D.Gaufreteau, H.Liu, X.Lin, A.Stich, B.Kuhn, F.Schuler, M.Kaiser, R.Brun, T.Schirmeister, C.Kisker, F.Diederich, W.Haap. Repurposing A Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams As Potent Rhodesain and Trypanosoma Brucei Inhibitors. J. Med. Chem. V. 61 3350 2018.
ISSN: ISSN 1520-4804
PubMed: 29590750
DOI: 10.1021/ACS.JMEDCHEM.7B01869