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

Protein crystallography data

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

Other elements in 6ex8:

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

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

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 6ex8

Go back to Fluorine Binding Sites List in 6ex8
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 6ex8

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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 6ex8

Go back to Fluorine Binding Sites List in 6ex8
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 6ex8

Go back to Fluorine Binding Sites List in 6ex8
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 6ex8

Go back to Fluorine Binding Sites List in 6ex8
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 6ex8

Go back to Fluorine Binding Sites List in 6ex8
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

Reference:

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
Page generated: Thu Aug 1 19:49:23 2024

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