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Fluorine in PDB 8pf3: Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)(4-Fluorophenyl)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)(4-Fluorophenyl)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)(4-Fluorophenyl)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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium, PDB code: 8pf3 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) 168.54 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 100.703, 63.742, 170.096, 90, 97.75, 90
R / Rfree (%) 17.9 / 22.4

Other elements in 8pf3:

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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium also contains other interesting chemical elements:

Chlorine (Cl) 8 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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium (pdb code 8pf3). 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 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium, PDB code: 8pf3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 1 out of 8 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)(4-Fluorophenyl)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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:48.2
occ:0.70
 F1 A:YJ6502 0.0 48.2 0.7
C1 A:YJ6502 1.4 51.1 0.7
C2 A:YJ6502 2.3 49.4 0.7
C41 A:YJ6502 2.3 50.7 0.7
O B:VAL58 3.1 28.8 1.0
CG1 B:VAL58 3.5 33.1 1.0
CA B:VAL58 3.5 29.2 1.0
C3 A:YJ6502 3.6 54.4 0.7
C40 A:YJ6502 3.6 52.9 0.7
CG B:LEU62 3.6 33.2 1.0
C B:VAL58 3.7 30.2 1.0
CD2 A:LEU399 3.8 55.9 1.0
CD2 B:LEU62 3.8 32.9 1.0
CB B:VAL58 3.9 32.3 1.0
C4 A:YJ6502 4.1 54.2 0.7
CB B:LYS61 4.2 35.0 1.0
CG2 B:VAL58 4.2 33.3 1.0
CD1 B:LEU62 4.3 35.0 1.0
CG B:LYS61 4.4 39.7 1.0
N B:LEU62 4.4 32.6 1.0
CB A:LEU399 4.5 44.9 1.0
O B:CYS57 4.8 30.2 1.0
N B:VAL58 4.8 28.8 1.0
CG A:LEU399 4.8 57.8 1.0
CB B:LEU62 4.8 33.5 1.0
CB A:PRO462 4.8 38.3 1.0
O A:HOH673 4.8 32.8 1.0
N B:PRO59 4.9 32.6 1.0
CG A:PRO462 4.9 37.0 1.0

Fluorine binding site 2 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 2 out of 8 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)(4-Fluorophenyl)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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:97.8
occ:0.70
 F2 A:YJ6502 0.0 97.8 0.7
C16 A:YJ6502 1.4 110.3 0.7
C15 A:YJ6502 2.3 108.7 0.7
C17 A:YJ6502 2.4 106.5 0.7
C14 A:YJ6502 3.6 105.1 0.7
C18 A:YJ6502 3.6 106.0 0.7
C13 A:YJ6502 4.1 104.3 0.7

Fluorine binding site 3 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 3 out of 8 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)(4-Fluorophenyl)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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:54.0
occ:0.70
 F1 B:YJ6502 0.0 54.0 0.7
C1 B:YJ6502 1.4 61.9 0.7
C41 B:YJ6502 2.3 60.4 0.7
C2 B:YJ6502 2.4 54.8 0.7
O A:VAL58 3.0 31.6 1.0
CG A:LEU62 3.5 37.2 1.0
CG1 A:VAL58 3.5 37.0 1.0
CD2 A:LEU62 3.5 37.6 1.0
C40 B:YJ6502 3.6 63.8 0.7
C3 B:YJ6502 3.6 58.3 0.7
CA A:VAL58 3.7 32.4 1.0
C A:VAL58 3.7 35.2 1.0
CB A:VAL58 4.1 36.8 1.0
CD1 A:LEU62 4.1 37.4 1.0
C4 B:YJ6502 4.1 62.0 0.7
CD2 B:LEU399 4.2 49.9 1.0
CB A:LYS61 4.2 32.8 1.0
N A:LEU62 4.3 31.5 1.0
CG A:LYS61 4.4 36.6 1.0
CG2 A:VAL58 4.6 39.0 1.0
CB A:LEU62 4.7 35.5 1.0
CG B:LEU399 4.8 51.4 1.0
CB B:LEU399 4.8 44.6 1.0
CG B:PRO462 4.9 41.5 1.0
O A:CYS57 4.9 27.3 1.0
CA A:LEU62 4.9 33.6 1.0
O B:HOH669 4.9 38.8 1.0
C A:LYS61 4.9 32.7 1.0
N A:PRO59 4.9 32.8 1.0
N A:VAL58 5.0 31.9 1.0
CB B:PRO462 5.0 41.1 1.0

Fluorine binding site 4 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 4 out of 8 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)(4-Fluorophenyl)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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:108.5
occ:0.70
 F2 B:YJ6502 0.0 108.5 0.7
C16 B:YJ6502 1.4 121.8 0.7
C15 B:YJ6502 2.3 121.1 0.7
C17 B:YJ6502 2.4 122.1 0.7
C14 B:YJ6502 3.6 125.5 0.7
C18 B:YJ6502 3.6 123.8 0.7
C13 B:YJ6502 4.1 126.7 0.7
C10 B:YJ6502 4.9 97.3 0.7

Fluorine binding site 5 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 5 out of 8 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)(4-Fluorophenyl)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)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:41.7
occ:0.70
 F1 C:YJ6502 0.0 41.7 0.7
C1 C:YJ6502 1.4 53.3 0.7
C41 C:YJ6502 2.3 53.3 0.7
C2 C:YJ6502 2.3 49.5 0.7
O D:VAL58 3.0 30.5 1.0
CG1 D:VAL58 3.5 37.0 1.0
C40 C:YJ6502 3.6 56.5 0.7
C3 C:YJ6502 3.6 52.9 0.7
CD2 D:LEU62 3.6 39.6 1.0
CG D:LEU62 3.7 38.1 1.0
CA D:VAL58 3.7 31.3 1.0
C D:VAL58 3.8 34.0 1.0
CD2 C:LEU399 3.9 43.0 1.0
CB D:LYS61 4.1 35.3 1.0
CB D:VAL58 4.1 31.1 1.0
C4 C:YJ6502 4.1 54.9 0.7
N D:LEU62 4.3 32.8 1.0
CG D:LYS61 4.4 41.5 1.0
CG2 D:VAL58 4.6 31.1 1.0
CD1 D:LEU62 4.6 38.9 1.0
CG C:LEU399 4.6 44.9 1.0
CB C:LEU399 4.7 40.3 1.0
O C:HOH608 4.8 43.3 1.0
CB D:LEU62 4.9 33.6 1.0
C D:LYS61 4.9 32.2 1.0
O D:CYS57 4.9 30.6 1.0
CB C:PRO462 4.9 44.3 1.0
CA D:LEU62 5.0 32.2 1.0
CA D:LYS61 5.0 33.4 1.0
N D:PRO59 5.0 31.2 1.0

Fluorine binding site 6 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 6 out of 8 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)(4-Fluorophenyl)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 6 of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:105.2
occ:0.70
 F2 C:YJ6502 0.0 105.2 0.7
C16 C:YJ6502 1.4 120.0 0.7
C15 C:YJ6502 2.3 124.6 0.7
C17 C:YJ6502 2.3 123.3 0.7
C18 C:YJ6502 3.6 130.0 0.7
C14 C:YJ6502 3.6 131.5 0.7
C13 C:YJ6502 4.1 133.8 0.7

Fluorine binding site 7 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 7 out of 8 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)(4-Fluorophenyl)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 7 of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:76.9
occ:0.90
 F1 D:YJ6502 0.0 76.9 0.9
C1 D:YJ6502 1.4 83.9 0.9
C41 D:YJ6502 2.3 81.6 0.9
C2 D:YJ6502 2.4 72.5 0.9
O C:VAL58 3.2 39.0 1.0
C3 D:YJ6502 3.6 75.7 0.9
C40 D:YJ6502 3.6 76.8 0.9
CA C:VAL58 3.7 35.2 1.0
CG C:LEU62 3.8 41.4 1.0
CG1 C:VAL58 3.9 37.6 1.0
C C:VAL58 3.9 38.2 1.0
CD2 C:LEU62 3.9 44.8 1.0
CB C:LYS61 4.0 39.0 1.0
C4 D:YJ6502 4.1 78.2 0.9
CG C:LYS61 4.1 43.3 1.0
CB C:VAL58 4.1 38.0 1.0
CD2 D:LEU399 4.2 56.7 1.0
CG2 C:VAL58 4.3 40.3 1.0
N C:LEU62 4.5 37.1 1.0
CD1 C:LEU62 4.5 42.2 1.0
CB D:LEU399 4.6 52.3 1.0
CG D:LEU399 4.7 54.4 1.0
CB D:PRO462 4.8 45.3 1.0
CG D:PRO462 4.8 46.0 1.0
O C:CYS57 4.9 43.8 1.0
N C:VAL58 4.9 36.0 1.0
CB C:LEU62 5.0 40.0 1.0
C C:LYS61 5.0 35.9 1.0

Fluorine binding site 8 out of 8 in 8pf3

Go back to Fluorine Binding Sites List in 8pf3
Fluorine binding site 8 out of 8 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)(4-Fluorophenyl)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 8 of Crystal Structure of Trypanosoma Brucei Trypanothione Reductase in Complex with 1-(3,4-Dichlorobenzyl)-4-(((5-((4-Fluorophenethyl) Carbamoyl)Furan-2-Yl)Methyl)(4-Fluorophenyl)Carbamoyl)-1-(3- Phenylpropyl)Piperazin-1-Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F502

b:141.9
occ:0.90
 F2 D:YJ6502 0.0 141.9 0.9
C16 D:YJ6502 1.4 154.9 0.9
C15 D:YJ6502 2.3 154.0 0.9
C17 D:YJ6502 2.3 154.7 0.9
C14 D:YJ6502 3.6 155.4 0.9
C18 D:YJ6502 3.6 155.8 0.9
C13 D:YJ6502 4.1 152.4 0.9
CB D:PHE396 5.0 57.5 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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