Chlorine 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:

Fluorine (F) 5 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium (pdb code 8pf5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium, PDB code: 8pf5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 8pf5

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Chlorine binding site 1 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:59.3
occ:0.25
 CL1 A:YJK502 0.0 59.3 0.2
C29 A:YJK502 1.7 56.8 0.2
C28 A:YJK502 2.7 57.1 0.2
C30 A:YJK502 2.7 59.0 0.2
CL2 A:YJK502 3.2 58.3 0.2
CD1 B:ILE106 3.2 34.1 1.0
CG1 B:ILE106 3.7 32.2 1.0
CG2 B:ILE106 3.7 31.4 1.0
C27 A:YJK502 4.0 58.5 0.2
C31 A:YJK502 4.0 61.2 0.2
CG2 B:VAL58 4.1 32.9 1.0
CG2 B:VAL53 4.3 24.7 1.0
CB B:ILE106 4.3 31.5 1.0
C26 A:YJK502 4.5 61.9 0.2
C33 A:YJK502 5.0 69.4 0.2
CG1 B:VAL58 5.0 33.0 1.0

Chlorine binding site 2 out of 10 in 8pf5

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Chlorine binding site 2 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:58.3
occ:0.25
 CL2 A:YJK502 0.0 58.3 0.2
C30 A:YJK502 1.7 59.0 0.2
C31 A:YJK502 2.7 61.2 0.2
C29 A:YJK502 2.7 56.8 0.2
CL1 A:YJK502 3.2 59.3 0.2
CG2 B:VAL53 3.4 24.7 1.0
OH B:TYR110 3.7 46.1 1.0
C26 A:YJK502 4.0 61.9 0.2
C28 A:YJK502 4.0 57.1 0.2
C27 A:YJK502 4.5 58.5 0.2
NE2 A:HIS461 4.6 33.0 1.0
CZ B:TYR110 4.8 45.7 1.0
CB B:VAL53 4.8 27.7 1.0
C33 A:YJK502 4.9 69.4 0.2
C32 A:YJK502 4.9 69.6 0.2
CG2 B:VAL58 4.9 32.9 1.0
CE1 A:HIS461 5.0 32.9 1.0

Chlorine binding site 3 out of 10 in 8pf5

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Chlorine binding site 3 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:72.9
occ:0.50
 CL1 B:YJK502 0.0 72.9 0.5
C29 B:YJK502 1.7 85.4 0.5
C28 B:YJK502 2.7 86.1 0.5
C30 B:YJK502 2.7 83.6 0.5
CL2 B:YJK502 3.1 73.9 0.5
C27 B:YJK502 4.0 85.9 0.5
C31 B:YJK502 4.0 84.7 0.5
CH2 A:TRP21 4.0 54.3 1.0
CZ3 A:TRP21 4.0 53.0 1.0
CG A:MET113 4.0 59.2 1.0
CB A:MET113 4.4 53.1 1.0
C21 B:YJK502 4.5 72.7 0.5
C26 B:YJK502 4.5 87.4 0.5
CE3 A:TRP21 4.6 48.1 1.0
CZ2 A:TRP21 4.6 51.4 1.0
SD A:MET113 4.8 74.0 1.0
C22 B:YJK502 5.0 72.7 0.5

Chlorine binding site 4 out of 10 in 8pf5

Go back to Chlorine Binding Sites List in 8pf5
Chlorine binding site 4 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:73.9
occ:0.50
 CL2 B:YJK502 0.0 73.9 0.5
C30 B:YJK502 1.7 83.6 0.5
C31 B:YJK502 2.7 84.7 0.5
C29 B:YJK502 2.7 85.4 0.5
CL1 B:YJK502 3.1 72.9 0.5
C28 B:YJK502 4.0 86.1 0.5
C26 B:YJK502 4.0 87.4 0.5
CE1 A:TYR110 4.1 57.1 1.0
OG A:SER109 4.3 53.9 1.0
CD1 A:TYR110 4.3 52.9 1.0
C27 B:YJK502 4.5 85.9 0.5
CB A:MET113 4.5 53.1 1.0
O A:SER109 4.6 46.7 1.0
CZ A:TYR110 4.8 55.2 1.0
CG A:MET113 4.8 59.2 1.0
SD A:MET113 4.8 74.0 1.0
C22 B:YJK502 4.9 72.7 0.5

Chlorine binding site 5 out of 10 in 8pf5

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Chlorine binding site 5 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:56.9
occ:0.00
 CL1 C:YJK502 0.0 56.9 0.0
CL1 C:YJK502 0.4 77.7 0.5
C29 C:YJK502 1.7 63.0 0.0
C29 C:YJK502 2.0 93.7 0.5
C28 C:YJK502 2.7 63.6 0.0
C30 C:YJK502 2.7 64.7 0.0
C28 C:YJK502 2.9 93.9 0.5
C30 C:YJK502 3.1 97.0 0.5
CL2 C:YJK502 3.2 64.4 0.0
CL2 C:YJK502 3.5 92.7 0.5
OE1 D:GLU18 3.8 39.4 1.0
CG2 D:ILE339 3.8 32.0 1.0
C27 C:YJK502 4.0 64.7 0.0
C31 C:YJK502 4.0 65.6 0.0
C27 C:YJK502 4.2 96.1 0.5
C31 C:YJK502 4.3 98.2 0.5
CD1 D:ILE339 4.4 33.5 1.0
CD D:GLU18 4.4 42.1 1.0
OE2 D:GLU18 4.5 38.9 1.0
C26 C:YJK502 4.5 65.4 0.0
CB C:SER470 4.7 48.7 1.0
C26 C:YJK502 4.8 97.2 0.5
CB D:ILE339 5.0 33.6 1.0

Chlorine binding site 6 out of 10 in 8pf5

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Chlorine binding site 6 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:77.7
occ:0.50
 CL1 C:YJK502 0.0 77.7 0.5
CL1 C:YJK502 0.4 56.9 0.0
C29 C:YJK502 1.5 63.0 0.0
C29 C:YJK502 1.7 93.7 0.5
C30 C:YJK502 2.4 64.7 0.0
C28 C:YJK502 2.5 63.6 0.0
C28 C:YJK502 2.7 93.9 0.5
C30 C:YJK502 2.7 97.0 0.5
CL2 C:YJK502 3.0 64.4 0.0
CL2 C:YJK502 3.2 92.7 0.5
C31 C:YJK502 3.7 65.6 0.0
C27 C:YJK502 3.7 64.7 0.0
OE1 D:GLU18 3.8 39.4 1.0
C27 C:YJK502 4.0 96.1 0.5
C31 C:YJK502 4.0 98.2 0.5
CG2 D:ILE339 4.1 32.0 1.0
C26 C:YJK502 4.2 65.4 0.0
C26 C:YJK502 4.5 97.2 0.5
CD D:GLU18 4.5 42.1 1.0
OE2 D:GLU18 4.5 38.9 1.0
CB C:SER470 4.5 48.7 1.0
CD1 D:ILE339 4.6 33.5 1.0

Chlorine binding site 7 out of 10 in 8pf5

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Chlorine binding site 7 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:64.4
occ:0.00
 CL2 C:YJK502 0.0 64.4 0.0
CL2 C:YJK502 0.5 92.7 0.5
C30 C:YJK502 1.7 64.7 0.0
C30 C:YJK502 1.8 97.0 0.5
C29 C:YJK502 2.6 93.7 0.5
C31 C:YJK502 2.7 65.6 0.0
C29 C:YJK502 2.7 63.0 0.0
C31 C:YJK502 2.9 98.2 0.5
CL1 C:YJK502 3.0 77.7 0.5
CB C:SER470 3.0 48.7 1.0
CL1 C:YJK502 3.2 56.9 0.0
OG C:SER470 3.3 48.0 1.0
C28 C:YJK502 4.0 93.9 0.5
C26 C:YJK502 4.0 65.4 0.0
C28 C:YJK502 4.0 63.6 0.0
C26 C:YJK502 4.2 97.2 0.5
CA C:SER470 4.4 48.4 1.0
C27 C:YJK502 4.5 64.7 0.0
C33 C:YJK502 4.5 66.8 0.0
C27 C:YJK502 4.6 96.1 0.5
C33 C:YJK502 4.6 84.4 0.5
O C:SER470 4.7 43.9 1.0
OE2 C:GLU467 5.0 68.7 1.0

Chlorine binding site 8 out of 10 in 8pf5

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Chlorine binding site 8 out of 10 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 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)Carbamoyl)-1-(3-Phenylpropyl)Piperazin-1- Ium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:92.7
occ:0.50
 CL2 C:YJK502 0.0 92.7 0.5
CL2 C:YJK502 0.5 64.4 0.0
C30 C:YJK502 1.7 97.0 0.5
C30 C:YJK502 1.7 64.7 0.0
C31 C:YJK502 2.5 65.6 0.0
C31 C:YJK502 2.7 98.2 0.5
C29 C:YJK502 2.7 93.7 0.5
C29 C:YJK502 2.9 63.0 0.0
CB C:SER470 3.0 48.7 1.0
CL1 C:YJK502 3.2 77.7 0.5
CL1 C:YJK502 3.5 56.9 0.0
OG C:SER470 3.5 48.0 1.0
C26 C:YJK502 3.8 65.4 0.0
C26 C:YJK502 4.0 97.2 0.5
C28 C:YJK502 4.0 93.9 0.5
C28 C:YJK502 4.1 63.6 0.0
CA C:SER470 4.4 48.4 1.0
O C:SER470 4.4 43.9 1.0
C33 C:YJK502 4.4 66.8 0.0
C27 C:YJK502 4.4 64.7 0.0
C27 C:YJK502 4.5 96.1 0.5
C33 C:YJK502 4.5 84.4 0.5
OE2 C:GLU467 4.7 68.7 1.0
C C:SER470 4.9 46.9 1.0
C25 C:YJK502 4.9 65.5 0.0

Chlorine binding site 9 out of 10 in 8pf5

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Chlorine binding site 9 out of 10 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl502

b:89.1
occ:0.40
 CL1 D:YJK502 0.0 89.1 0.4
C29 D:YJK502 1.7 76.5 0.4
C28 D:YJK502 2.7 73.5 0.4
C30 D:YJK502 2.7 76.7 0.4
CL2 D:YJK502 3.1 88.8 0.4
C2 D:YJK502 3.2 59.5 1.0
CG2 C:VAL58 3.5 33.2 1.0
C3 D:YJK502 3.7 61.4 1.0
CE1 D:HIS461 3.7 43.1 1.0
O D:HOH610 3.8 37.0 1.0
NE2 D:HIS461 3.9 38.1 1.0
C27 D:YJK502 4.0 73.6 0.4
C31 D:YJK502 4.0 77.7 0.4
C1 D:YJK502 4.4 62.9 1.0
C26 D:YJK502 4.5 77.6 0.4
CB C:VAL58 4.6 32.7 1.0
F1 D:YJK502 4.6 60.9 1.0
CG1 C:VAL58 4.7 31.0 1.0
CB D:PRO462 4.7 46.0 1.0
ND1 D:HIS461 4.9 43.2 1.0
CD2 D:LEU399 5.0 46.1 1.0

Chlorine binding site 10 out of 10 in 8pf5

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Chlorine binding site 10 out of 10 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl502

b:88.8
occ:0.40
 CL2 D:YJK502 0.0 88.8 0.4
C30 D:YJK502 1.7 76.7 0.4
C31 D:YJK502 2.7 77.7 0.4
C29 D:YJK502 2.7 76.5 0.4
C9 D:YJK502 3.1 54.0 1.0
CL1 D:YJK502 3.1 89.1 0.4
CD1 D:LEU399 3.4 48.1 1.0
C8 D:YJK502 3.4 50.5 1.0
C10 D:YJK502 3.5 54.8 1.0
CD2 D:LEU399 3.7 46.1 1.0
O2 D:YJK502 3.9 51.9 1.0
C11 D:YJK502 3.9 55.6 1.0
C2 D:YJK502 3.9 59.5 1.0
C26 D:YJK502 4.0 77.6 0.4
C28 D:YJK502 4.0 73.5 0.4
C7 D:YJK502 4.0 53.2 1.0
CG D:LEU399 4.1 47.4 1.0
O3 D:YJK502 4.2 52.6 1.0
C3 D:YJK502 4.2 61.4 1.0
C27 D:YJK502 4.5 73.6 0.4
C14 D:YJK502 4.5 81.1 0.4
CB D:LEU399 4.7 41.4 1.0
N2 D:YJK502 4.8 64.1 1.0
N3 D:YJK502 4.9 80.4 0.4
C1 D:YJK502 4.9 62.9 1.0
N1 D:YJK502 5.0 54.1 1.0
C12 D:YJK502 5.0 59.1 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 11:32:58 2024

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