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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy