Chlorine 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:

Fluorine (F) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8pf3

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:157.1
occ:0.70
 CL1 A:YJ6502 0.0 157.1 0.7
C35 A:YJ6502 1.7 154.7 0.7
C34 A:YJ6502 2.7 149.1 0.7
C36 A:YJ6502 2.7 150.0 0.7
C3 A:YJ6502 3.0 54.4 0.7
OE2 A:GLU466 3.1 46.5 1.0
CL2 A:YJ6502 3.2 127.2 0.7
C5 A:YJ6502 3.3 56.7 0.7
O A:HOH620 3.3 45.2 1.0
C4 A:YJ6502 3.5 54.2 0.7
CE1 A:HIS461 3.6 44.8 1.0
ND1 A:HIS461 3.7 38.4 1.0
O2 A:YJ6502 3.9 71.1 0.7
O A:THR463 4.0 31.5 1.0
C33 A:YJ6502 4.0 142.1 0.7
CD A:GLU466 4.0 44.8 1.0
C37 A:YJ6502 4.0 148.2 0.7
N1 A:YJ6502 4.1 59.8 0.7
CB A:PRO462 4.1 38.3 1.0
C2 A:YJ6502 4.1 49.4 0.7
CA A:PRO462 4.2 35.6 1.0
C6 A:YJ6502 4.2 54.9 0.7
N A:THR463 4.3 34.1 1.0
C7 A:YJ6502 4.4 63.1 0.7
C32 A:YJ6502 4.5 146.8 0.7
C8 A:YJ6502 4.5 67.7 0.7
CG A:GLU466 4.6 40.5 1.0
C A:PRO462 4.7 34.3 1.0
OE1 A:GLU466 4.8 43.3 1.0
C40 A:YJ6502 4.8 52.9 0.7
C11 A:YJ6502 4.8 80.4 0.7
NE2 A:HIS461 4.8 41.8 1.0
C A:THR463 4.9 37.0 1.0
CG A:HIS461 4.9 36.8 1.0
O3 A:YJ6502 5.0 50.2 0.7
OE1 A:GLU467 5.0 55.0 1.0
C12 A:YJ6502 5.0 86.6 0.7

Chlorine binding site 2 out of 8 in 8pf3

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:127.2
occ:0.70
 CL2 A:YJ6502 0.0 127.2 0.7
C36 A:YJ6502 1.7 150.0 0.7
C37 A:YJ6502 2.7 148.2 0.7
C35 A:YJ6502 2.7 154.7 0.7
CL1 A:YJ6502 3.2 157.1 0.7
O2 A:YJ6502 3.9 71.1 0.7
C11 A:YJ6502 4.0 80.4 0.7
C32 A:YJ6502 4.0 146.8 0.7
C34 A:YJ6502 4.0 149.1 0.7
C12 A:YJ6502 4.0 86.6 0.7
C3 A:YJ6502 4.1 54.4 0.7
CE1 A:HIS461 4.1 44.8 1.0
C2 A:YJ6502 4.3 49.4 0.7
C33 A:YJ6502 4.5 142.1 0.7
C8 A:YJ6502 4.5 67.7 0.7
C10 A:YJ6502 4.6 73.3 0.7
C9 A:YJ6502 4.9 69.3 0.7
CG2 B:VAL58 4.9 33.3 1.0
NE2 A:HIS461 5.0 41.8 1.0

Chlorine binding site 3 out of 8 in 8pf3

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:129.0
occ:0.70
 CL1 B:YJ6502 0.0 129.0 0.7
C35 B:YJ6502 1.7 129.4 0.7
C34 B:YJ6502 2.7 125.4 0.7
C36 B:YJ6502 2.7 135.4 0.7
CL2 B:YJ6502 3.1 121.2 0.7
CG A:PRO336 3.1 34.4 1.0
OE1 B:GLU466 3.2 44.4 1.0
CB B:HIS461 3.5 36.0 1.0
CG B:HIS461 3.6 39.5 1.0
CD1 A:ILE339 3.7 32.2 1.0
CB A:PRO336 3.7 35.9 1.0
CG2 A:THR335 3.7 29.9 1.0
ND1 B:HIS461 3.7 42.9 1.0
CA A:PRO336 3.8 33.6 1.0
CD A:PRO336 3.9 33.9 1.0
N A:PRO336 3.9 34.7 1.0
C33 B:YJ6502 4.0 129.4 0.7
C37 B:YJ6502 4.0 138.5 0.7
CD2 B:HIS461 4.3 42.5 1.0
CD B:GLU466 4.3 44.2 1.0
CE1 B:HIS461 4.4 44.7 1.0
C32 B:YJ6502 4.5 142.9 0.7
C A:THR335 4.5 31.2 1.0
CB A:THR335 4.7 31.0 1.0
NE2 B:HIS461 4.8 43.0 1.0
CA B:HIS461 4.8 36.5 1.0
OE2 B:GLU466 4.8 40.3 1.0
CG1 A:ILE339 4.9 32.3 1.0

Chlorine binding site 4 out of 8 in 8pf3

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:121.2
occ:0.70
 CL2 B:YJ6502 0.0 121.2 0.7
C36 B:YJ6502 1.7 135.4 0.7
C37 B:YJ6502 2.7 138.5 0.7
C35 B:YJ6502 2.7 129.4 0.7
CL1 B:YJ6502 3.1 129.0 0.7
OE1 B:GLU466 3.3 44.4 1.0
OG B:SER470 3.5 61.1 1.0
C34 B:YJ6502 4.0 125.4 0.7
C32 B:YJ6502 4.0 142.9 0.7
CD B:GLU466 4.2 44.2 1.0
C33 B:YJ6502 4.5 129.4 0.7
CG B:GLU466 4.5 40.2 1.0
CA B:GLY459 4.5 36.4 1.0
CB B:GLU466 4.5 37.9 1.0
O B:GLU466 4.7 38.1 1.0
N B:GLY459 4.9 38.9 1.0
CB B:SER470 4.9 50.3 1.0
CD1 A:ILE339 4.9 32.2 1.0
C22 B:YJ6502 5.0 159.2 0.7

Chlorine binding site 5 out of 8 in 8pf3

Go back to Chlorine Binding Sites List in 8pf3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:145.2
occ:0.70
 CL1 C:YJ6502 0.0 145.2 0.7
C35 C:YJ6502 1.7 172.2 0.7
C34 C:YJ6502 2.7 176.6 0.7
C36 C:YJ6502 2.7 177.6 0.7
CG2 D:THR335 3.0 31.8 1.0
CL2 C:YJ6502 3.1 172.0 0.7
OG D:SER14 3.2 34.5 1.0
O D:HOH609 3.8 43.2 1.0
SG D:CYS52 3.8 58.4 1.0
CB D:CYS52 4.0 43.1 1.0
C33 C:YJ6502 4.0 181.2 0.7
C37 C:YJ6502 4.0 182.2 0.7
OG1 D:THR335 4.0 33.1 1.0
CB D:SER14 4.0 32.0 1.0
NE2 C:HIS461 4.1 43.3 1.0
CD1 D:ILE339 4.1 33.0 1.0
CB D:THR335 4.2 31.9 1.0
CA D:SER14 4.5 30.3 1.0
CD2 C:HIS461 4.5 39.6 1.0
C32 C:YJ6502 4.5 184.2 0.7
O D:HOH670 4.5 38.6 1.0
CE1 C:HIS461 4.6 42.0 1.0
O C:HOH661 4.8 47.1 1.0
CG1 D:ILE339 4.9 34.2 1.0
CG2 D:VAL53 4.9 27.8 1.0

Chlorine binding site 6 out of 8 in 8pf3

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:172.0
occ:0.70
 CL2 C:YJ6502 0.0 172.0 0.7
C36 C:YJ6502 1.7 177.6 0.7
O D:HOH764 2.4 64.7 1.0
C35 C:YJ6502 2.7 172.2 0.7
C37 C:YJ6502 2.7 182.2 0.7
CL1 C:YJ6502 3.1 145.2 0.7
NE2 C:HIS461 3.4 43.3 1.0
CG2 D:VAL53 3.5 27.8 1.0
CG2 D:VAL58 3.6 31.1 1.0
CE1 C:HIS461 3.7 42.0 1.0
C34 C:YJ6502 4.0 176.6 0.7
C32 C:YJ6502 4.0 184.2 0.7
SG D:CYS52 4.2 58.4 1.0
C33 C:YJ6502 4.5 181.2 0.7
CD2 C:HIS461 4.6 39.6 1.0
O D:HOH609 4.6 43.2 1.0
CB D:VAL53 4.7 27.6 1.0
CA D:VAL53 4.7 29.0 1.0
CB D:CYS52 4.7 43.1 1.0
N D:VAL53 4.7 29.2 1.0
OH D:TYR110 4.9 44.8 1.0
ND1 C:HIS461 4.9 42.4 1.0

Chlorine binding site 7 out of 8 in 8pf3

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Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:200.3
occ:0.90
 CL1 D:YJ6502 0.0 200.3 0.9
C35 D:YJ6502 1.7 209.6 0.9
C34 D:YJ6502 2.7 206.9 0.9
C36 D:YJ6502 2.7 212.8 0.9
CL2 D:YJ6502 3.2 199.6 0.9
CD1 C:ILE339 3.6 61.0 1.0
C33 D:YJ6502 4.0 213.8 0.9
C37 D:YJ6502 4.0 219.1 0.9
CG2 C:THR335 4.2 46.9 1.0
OH C:TYR110 4.5 69.2 1.0
C32 D:YJ6502 4.5 222.2 0.9
NE2 D:HIS461 4.6 53.8 1.0
CE1 D:HIS461 4.8 51.5 1.0
CG1 C:ILE339 4.8 60.8 1.0
OG C:SER14 4.9 61.4 1.0

Chlorine binding site 8 out of 8 in 8pf3

Go back to Chlorine Binding Sites List in 8pf3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl502

b:199.6
occ:0.90
 CL2 D:YJ6502 0.0 199.6 0.9
C36 D:YJ6502 1.7 212.8 0.9
C37 D:YJ6502 2.7 219.1 0.9
C35 D:YJ6502 2.7 209.6 0.9
CL1 D:YJ6502 3.2 200.3 0.9
OH C:TYR110 3.7 69.2 1.0
C32 D:YJ6502 4.0 222.2 0.9
C34 D:YJ6502 4.0 206.9 0.9
CD1 C:ILE339 4.1 61.0 1.0
O C:HOH702 4.2 55.2 1.0
OE1 C:GLU18 4.2 67.0 1.0
C33 D:YJ6502 4.5 213.8 0.9
O C:SER14 4.5 55.4 1.0
CG1 C:ILE339 4.6 60.8 1.0
CZ C:TYR110 4.9 65.3 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: Tue Jul 30 11:32:51 2024

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