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Fluorine in PDB 8pf4: Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium

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

All present enzymatic activity of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium, PDB code: 8pf4 was solved by C.Exertier, A.Ilari, A.Fiorillo, L.Antonelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 167.74 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.922, 63.635, 169.104, 90, 97.29, 90
R / Rfree (%) 17.9 / 22.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium (pdb code 8pf4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium, PDB code: 8pf4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 1 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:21.1
occ:1.00
 F1 A:YIA502 0.0 21.1 1.0
C1 A:YIA502 1.4 19.5 1.0
C2 A:YIA502 2.3 18.3 1.0
C35 A:YIA502 2.4 19.0 1.0
CG1 B:VAL58 3.4 10.9 1.0
O B:VAL58 3.5 10.4 1.0
CD2 A:LEU399 3.5 23.6 1.0
CG B:LEU62 3.6 11.3 1.0
C3 A:YIA502 3.6 18.8 1.0
C34 A:YIA502 3.6 19.4 1.0
CD2 B:LEU62 3.8 11.7 1.0
CA B:VAL58 3.8 10.9 1.0
CD1 B:LEU62 3.9 11.7 1.0
CB B:VAL58 4.0 10.7 1.0
CB A:LEU399 4.0 18.9 1.0
C B:VAL58 4.0 10.6 1.0
C4 A:YIA502 4.1 19.1 1.0
CG2 B:VAL58 4.3 10.7 1.0
CG A:LEU399 4.4 22.9 1.0
CB B:LYS61 4.5 11.4 1.0
N B:LEU62 4.8 10.5 1.0
O A:HOH774 4.9 15.8 1.0
CB B:LEU62 4.9 11.2 1.0
CG B:LYS61 4.9 12.2 1.0

Fluorine binding site 2 out of 8 in 8pf4

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Fluorine binding site 2 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:60.5
occ:1.00
 F2 A:YIA502 0.0 60.5 1.0
C16 A:YIA502 1.4 57.7 1.0
C17 A:YIA502 2.3 59.5 1.0
C15 A:YIA502 2.3 56.4 1.0
CG2 B:VAL58 3.2 10.7 1.0
C18 A:YIA502 3.6 57.2 1.0
C14 A:YIA502 3.6 54.6 1.0
CD1 B:ILE106 3.9 16.1 1.0
C13 A:YIA502 4.1 53.4 1.0
O A:HOH771 4.2 21.6 1.0
CD2 A:LEU399 4.2 23.6 1.0
C35 A:YIA502 4.2 19.0 1.0
CB B:VAL58 4.4 10.7 1.0
CG1 B:VAL58 4.4 10.9 1.0
OH B:TYR110 4.7 18.4 0.1
CG1 B:ILE106 4.7 16.2 1.0
CE1 A:HIS461 4.8 14.8 1.0
CG2 B:VAL53 4.9 13.3 1.0
C34 A:YIA502 4.9 19.4 1.0
NE2 A:HIS461 4.9 16.1 1.0

Fluorine binding site 3 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 3 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:23.9
occ:1.00
 F1 A:YIA510 0.0 23.9 1.0
C1 A:YIA510 1.4 24.3 1.0
C2 A:YIA510 2.3 23.0 1.0
C35 A:YIA510 2.3 22.2 1.0
O A:VAL58 3.1 12.3 1.0
CG1 A:VAL58 3.4 13.2 1.0
CG A:LEU62 3.5 13.5 1.0
CD2 A:LEU62 3.6 13.7 1.0
C34 A:YIA510 3.6 22.3 1.0
C3 A:YIA510 3.6 22.7 1.0
CA A:VAL58 3.7 12.7 1.0
C A:VAL58 3.7 12.5 1.0
CD1 B:LEU399 3.9 22.8 1.0
CB A:VAL58 4.0 13.3 1.0
CD1 A:LEU62 4.1 14.2 1.0
C4 A:YIA510 4.1 22.2 1.0
CB B:LEU399 4.4 20.2 1.0
CB A:LYS61 4.4 12.4 1.0
CG2 A:VAL58 4.5 14.3 1.0
CG B:LEU399 4.5 22.5 1.0
N A:LEU62 4.6 11.2 1.0
CB A:LEU62 4.7 12.2 1.0
CG A:LYS61 4.7 14.1 1.0
N A:PRO59 4.9 12.0 1.0

Fluorine binding site 4 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 4 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:66.0
occ:1.00
 F2 A:YIA510 0.0 66.0 1.0
C16 A:YIA510 1.4 62.2 1.0
C17 A:YIA510 2.3 63.4 1.0
C15 A:YIA510 2.3 59.7 1.0
CG2 A:VAL58 3.3 14.3 1.0
C18 A:YIA510 3.6 63.1 1.0
C14 A:YIA510 3.6 60.6 1.0
CD1 A:ILE106 4.1 13.0 1.0
C13 A:YIA510 4.1 59.6 1.0
CE1 B:HIS461 4.3 13.7 1.0
C35 A:YIA510 4.4 22.2 1.0
CG1 A:VAL58 4.5 13.2 1.0
CB A:VAL58 4.5 13.3 1.0
NE2 B:HIS461 4.6 13.5 1.0
CD1 B:LEU399 4.7 22.8 1.0
CG2 A:VAL53 4.9 11.6 1.0
C34 A:YIA510 4.9 22.3 1.0
CG1 A:ILE106 4.9 12.9 1.0

Fluorine binding site 5 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 5 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:22.9
occ:0.90
 F1 D:YIA501 0.0 22.9 0.9
C1 D:YIA501 1.3 22.4 0.9
C2 D:YIA501 2.3 21.8 0.9
C35 D:YIA501 2.3 21.7 0.9
O D:VAL58 3.3 12.7 1.0
CG1 D:VAL58 3.5 13.5 1.0
C3 D:YIA501 3.6 21.8 0.9
C34 D:YIA501 3.6 22.5 0.9
CD2 D:LEU62 3.6 15.5 1.0
CG D:LEU62 3.7 14.9 1.0
CA D:VAL58 3.7 13.2 1.0
C D:VAL58 3.9 13.7 1.0
CD2 C:LEU399 3.9 23.7 1.0
CB D:VAL58 4.0 12.5 1.0
C4 D:YIA501 4.1 23.1 0.9
CB D:LYS61 4.2 15.4 1.0
CG2 D:VAL58 4.3 12.1 1.0
CD1 D:LEU62 4.3 14.8 1.0
CB C:LEU399 4.4 20.0 1.0
N D:LEU62 4.5 12.8 1.0
CG D:LYS61 4.7 17.3 1.0
CG C:LEU399 4.8 23.0 1.0
CB D:LEU62 4.9 14.6 1.0
CB C:PRO462 4.9 15.8 1.0
CG C:PRO462 4.9 16.4 1.0
O D:CYS57 5.0 12.7 1.0

Fluorine binding site 6 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 6 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 6 of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:52.6
occ:0.90
 F2 D:YIA501 0.0 52.6 0.9
C16 D:YIA501 1.4 48.3 0.9
C17 D:YIA501 2.3 49.8 0.9
C15 D:YIA501 2.3 47.8 0.9
CG2 D:VAL58 3.1 12.1 1.0
C18 D:YIA501 3.6 50.8 0.9
C14 D:YIA501 3.6 47.9 0.9
CD1 D:ILE106 3.7 13.6 1.0
O C:HOH654 3.9 31.2 1.0
C13 D:YIA501 4.1 48.3 0.9
CB D:VAL58 4.3 12.5 1.0
CG1 D:VAL58 4.4 13.5 1.0
CD2 C:LEU399 4.5 23.7 1.0
C35 D:YIA501 4.6 21.7 0.9
CG2 D:VAL53 4.6 13.6 1.0
CE1 C:HIS461 4.7 15.5 1.0
CG1 D:ILE106 4.8 13.7 1.0
NE2 C:HIS461 4.9 14.7 1.0
C3 C:PEG505 5.0 66.8 1.0

Fluorine binding site 7 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 7 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 7 of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:29.8
occ:1.00
 F1 D:YIA503 0.0 29.8 1.0
C1 D:YIA503 1.4 28.8 1.0
C35 D:YIA503 2.3 27.9 1.0
C2 D:YIA503 2.4 28.1 1.0
O C:VAL58 3.4 17.4 1.0
CG1 C:VAL58 3.5 15.7 1.0
C34 D:YIA503 3.6 27.4 1.0
CG C:LEU62 3.6 14.4 1.0
C3 D:YIA503 3.6 27.2 1.0
CD2 C:LEU62 3.8 15.6 1.0
CA C:VAL58 3.8 16.8 1.0
CB D:LEU399 4.0 30.0 1.0
C C:VAL58 4.0 17.6 1.0
CB C:VAL58 4.1 16.4 1.0
CD1 C:LEU62 4.1 14.8 1.0
CG D:LEU399 4.1 35.1 1.0
C4 D:YIA503 4.1 26.7 1.0
CG2 C:VAL58 4.3 16.0 1.0
CB C:LYS61 4.6 14.3 0.6
CB C:LYS61 4.6 13.7 0.4
CG C:LYS61 4.7 14.2 0.6
N C:LEU62 4.7 14.5 1.0
CD1 D:LEU399 4.8 40.5 1.0
CB C:LEU62 4.9 14.4 1.0

Fluorine binding site 8 out of 8 in 8pf4

Go back to Fluorine Binding Sites List in 8pf4
Fluorine binding site 8 out of 8 in the Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-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 8 of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 4-(((5-((4-Fluorophenethyl)Carbamoyl)Furan-2-Yl)Methyl) (4-Fluorophenyl)Carbamoyl)-1-Methyl-1-(3-Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:50.5
occ:1.00
 F2 D:YIA503 0.0 50.5 1.0
C16 D:YIA503 1.4 49.5 1.0
C17 D:YIA503 2.3 48.8 1.0
C15 D:YIA503 2.3 50.1 1.0
CG2 C:VAL58 3.1 16.0 1.0
C18 D:YIA503 3.6 48.4 1.0
C14 D:YIA503 3.6 49.6 1.0
CD1 C:ILE106 4.1 25.4 1.0
C13 D:YIA503 4.1 48.5 1.0
CB C:VAL58 4.3 16.4 1.0
CG1 C:VAL58 4.3 15.7 1.0
C35 D:YIA503 4.3 27.9 1.0
OH C:TYR110 4.6 52.0 1.0
CE1 D:HIS461 4.6 22.3 1.0
NE2 D:HIS461 4.8 21.8 1.0
CG1 C:ILE106 4.8 24.4 1.0
CG2 C:VAL53 5.0 20.0 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: Wed Jul 16 06:30:00 2025

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