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Fluorine in PDB 8pf5: Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium

Enzymatic activity of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium:
1.8.1.12;

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium, PDB code: 8pf5 was solved by C.Exertier, L.Antonelli, A.Fiorillo, A.Ilari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.83 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.96, 63.311, 169.112, 90, 98.4, 90
R / Rfree (%) 19 / 25.7

Other elements in 8pf5:

The structure of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium (pdb code 8pf5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium, PDB code: 8pf5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 8pf5

Go back to Fluorine Binding Sites List in 8pf5
Fluorine binding site 1 out of 5 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium


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 Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:59.5
occ:1.00
 F1 A:YJK502 0.0 59.5 1.0
C1 A:YJK502 1.4 57.7 1.0
C35 A:YJK502 2.3 62.6 1.0
C2 A:YJK502 2.3 54.9 1.0
CD2 B:LEU62 3.2 29.6 1.0
CG B:LEU62 3.3 28.0 1.0
CD2 A:LEU399 3.3 44.9 1.0
O B:VAL58 3.5 34.0 1.0
CG1 B:VAL58 3.6 33.0 1.0
C34 A:YJK502 3.6 61.2 1.0
C3 A:YJK502 3.6 56.5 1.0
CD1 B:LEU62 3.9 29.2 1.0
CB A:LEU399 3.9 39.8 1.0
C B:VAL58 4.0 32.5 1.0
CA B:VAL58 4.1 33.0 1.0
C4 A:YJK502 4.1 61.0 1.0
CG A:LEU399 4.3 43.0 1.0
CB B:VAL58 4.3 32.4 1.0
N B:LEU62 4.5 26.2 1.0
CG2 B:VAL58 4.6 32.9 1.0
CB B:LYS61 4.6 29.8 1.0
CB B:LEU62 4.7 25.5 1.0
CG B:LYS61 4.9 33.1 1.0
O A:HOH630 5.0 27.3 1.0

Fluorine binding site 2 out of 5 in 8pf5

Go back to Fluorine Binding Sites List in 8pf5
Fluorine binding site 2 out of 5 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium


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 Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:51.6
occ:1.00
 F1 B:YJK502 0.0 51.6 1.0
C1 B:YJK502 1.4 51.7 1.0
C35 B:YJK502 2.3 53.4 1.0
C2 B:YJK502 2.3 51.9 1.0
O A:VAL58 3.3 29.6 1.0
C34 B:YJK502 3.6 57.4 1.0
C3 B:YJK502 3.6 55.0 1.0
CG A:LEU62 3.7 36.8 1.0
CD2 A:LEU62 3.7 37.0 1.0
CA A:VAL58 3.7 27.5 1.0
CG1 A:VAL58 3.8 30.5 1.0
C A:VAL58 3.9 29.4 1.0
CD2 B:LEU399 3.9 47.3 1.0
CB A:VAL58 4.1 29.5 1.0
C4 B:YJK502 4.1 56.2 1.0
CB A:LYS61 4.2 33.2 1.0
CG2 A:VAL58 4.3 31.4 1.0
CB B:LEU399 4.3 38.4 1.0
CD1 A:LEU62 4.3 36.6 1.0
CG A:LYS61 4.5 37.3 1.0
N A:LEU62 4.6 30.9 1.0
CG B:LEU399 4.8 45.5 1.0
CB A:LEU62 4.9 35.7 1.0
CB B:PRO462 5.0 37.7 1.0

Fluorine binding site 3 out of 5 in 8pf5

Go back to Fluorine Binding Sites List in 8pf5
Fluorine binding site 3 out of 5 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium


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 Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:49.2
occ:0.40
 F1 C:YJK502 0.0 49.2 0.4
F1 C:YJK502 0.3 57.8 0.5
C1 C:YJK502 1.3 57.1 0.5
C1 C:YJK502 1.4 48.1 0.4
C35 C:YJK502 2.2 58.4 0.5
C2 C:YJK502 2.3 56.8 0.5
C35 C:YJK502 2.3 48.5 0.4
C2 C:YJK502 2.3 47.6 0.4
CD2 D:LEU62 3.4 39.6 1.0
O D:VAL58 3.4 38.0 1.0
C34 C:YJK502 3.5 58.2 0.5
C3 C:YJK502 3.5 58.8 0.5
CG D:LEU62 3.6 38.4 1.0
C34 C:YJK502 3.6 47.7 0.4
C3 C:YJK502 3.6 48.6 0.4
CG1 D:VAL58 3.9 33.3 1.0
CA D:VAL58 4.0 33.6 1.0
C4 C:YJK502 4.0 58.4 0.5
CD2 C:LEU399 4.0 51.9 1.0
C D:VAL58 4.0 36.4 1.0
C4 C:YJK502 4.1 48.3 0.4
CB C:LEU399 4.2 45.9 1.0
CB D:LYS61 4.2 37.9 1.0
N D:LEU62 4.3 31.3 1.0
CB D:VAL58 4.4 31.9 1.0
CD1 D:LEU62 4.4 42.3 1.0
CG C:LEU399 4.5 48.5 1.0
CG D:LYS61 4.5 45.1 1.0
CG2 D:VAL58 4.7 31.8 1.0
CB D:LEU62 4.7 36.4 1.0
CA D:LEU62 4.9 31.6 1.0
C D:LYS61 4.9 32.1 1.0

Fluorine binding site 4 out of 5 in 8pf5

Go back to Fluorine Binding Sites List in 8pf5
Fluorine binding site 4 out of 5 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium


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 Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:57.8
occ:0.50
 F1 C:YJK502 0.0 57.8 0.5
F1 C:YJK502 0.3 49.2 0.4
C1 C:YJK502 1.4 57.1 0.5
C1 C:YJK502 1.5 48.1 0.4
C35 C:YJK502 2.3 58.4 0.5
C2 C:YJK502 2.3 56.8 0.5
C2 C:YJK502 2.4 47.6 0.4
C35 C:YJK502 2.5 48.5 0.4
O D:VAL58 3.2 38.0 1.0
CD2 D:LEU62 3.5 39.6 1.0
C34 C:YJK502 3.6 58.2 0.5
C3 C:YJK502 3.6 58.8 0.5
CG D:LEU62 3.6 38.4 1.0
C3 C:YJK502 3.7 48.6 0.4
CG1 D:VAL58 3.7 33.3 1.0
CA D:VAL58 3.7 33.6 1.0
C34 C:YJK502 3.7 47.7 0.4
C D:VAL58 3.8 36.4 1.0
CD2 C:LEU399 4.1 51.9 1.0
C4 C:YJK502 4.1 58.4 0.5
CB D:VAL58 4.1 31.9 1.0
CB D:LYS61 4.1 37.9 1.0
C4 C:YJK502 4.2 48.3 0.4
N D:LEU62 4.3 31.3 1.0
CB C:LEU399 4.4 45.9 1.0
CD1 D:LEU62 4.4 42.3 1.0
CG2 D:VAL58 4.4 31.8 1.0
CG D:LYS61 4.5 45.1 1.0
CG C:LEU399 4.6 48.5 1.0
CB D:LEU62 4.8 36.4 1.0
CA D:LEU62 4.9 31.6 1.0
C D:LYS61 4.9 32.1 1.0
CB C:PRO462 5.0 47.0 1.0
N D:PRO59 5.0 37.5 1.0
O D:CYS57 5.0 35.0 1.0

Fluorine binding site 5 out of 5 in 8pf5

Go back to Fluorine Binding Sites List in 8pf5
Fluorine binding site 5 out of 5 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium


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 Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:60.9
occ:1.00
 F1 D:YJK502 0.0 60.9 1.0
C1 D:YJK502 1.4 62.9 1.0
C2 D:YJK502 2.3 59.5 1.0
C35 D:YJK502 2.3 64.0 1.0
O C:VAL58 3.4 31.7 1.0
CD2 D:LEU399 3.5 46.1 1.0
CD2 C:LEU62 3.5 37.6 1.0
CG1 C:VAL58 3.6 31.0 1.0
C3 D:YJK502 3.6 61.4 1.0
C34 D:YJK502 3.6 64.6 1.0
CG C:LEU62 3.6 33.9 1.0
CA C:VAL58 3.9 32.0 1.0
C C:VAL58 4.0 33.4 1.0
C4 D:YJK502 4.1 61.3 1.0
CB C:LYS61 4.1 32.9 1.0
CB D:LEU399 4.1 41.4 1.0
CB C:VAL58 4.2 32.7 1.0
CD1 C:LEU62 4.3 37.6 1.0
CG C:LYS61 4.4 36.8 1.0
CG D:LEU399 4.5 47.4 1.0
CG2 C:VAL58 4.6 33.2 1.0
CL1 D:YJK502 4.6 89.1 0.4
N C:LEU62 4.7 33.6 1.0
CB C:LEU62 4.9 31.8 1.0

Reference:

C.Exertier, A.Salerno, L.Antonelli, A.Fiorillo, R.Ocello, F.Seghetti, J.Caciolla, E.Uliassi, M.Masetti, E.Fiorentino, S.Orsini, T.Di Muccio, A.Ilari, M.L.Bolognesi. Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors For Leishmaniasis. J.Med.Chem. V. 67 402 2024.
ISSN: ISSN 0022-2623
PubMed: 38164929
DOI: 10.1021/ACS.JMEDCHEM.3C01439
Page generated: Fri Aug 2 21:59:57 2024

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