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Arsenic in PDB 4zt2: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575), PDB code: 4zt2 was solved by C.-Y.Koh, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.35 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.068, 106.070, 207.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.8

Other elements in 4zt2:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) (pdb code 4zt2). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575), PDB code: 4zt2:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4zt2

Go back to Arsenic Binding Sites List in 4zt2
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:54.5
occ:0.70
 AS A:CAS470 0.0 54.5 0.7
CE2 A:CAS470 2.0 57.1 0.7
CE1 A:CAS470 2.0 56.1 0.7
SG A:CAS470 2.2 50.5 1.0
CB A:CAS470 3.1 44.5 1.0
CA A:CAS470 3.6 41.5 1.0
O A:ALA460 3.7 38.8 1.0
CA A:PRO462 3.8 39.7 1.0
N A:PRO462 3.8 39.1 1.0
C A:ILE461 3.9 36.8 1.0
O A:ILE461 3.9 35.4 1.0
O A:HIS469 4.0 41.2 1.0
C A:ALA460 4.0 37.7 1.0
N A:CAS470 4.1 41.7 1.0
CG A:PRO462 4.3 42.8 1.0
C A:HIS469 4.3 41.7 1.0
CB A:ALA460 4.3 37.2 1.0
CD A:PRO462 4.4 41.5 1.0
CB A:ARG453 4.4 49.7 1.0
CB A:PRO462 4.4 41.5 1.0
N A:ILE461 4.5 36.4 1.0
CA A:ALA460 4.6 38.5 1.0
N A:ALA460 4.7 41.5 1.0
CA A:ILE461 4.8 36.6 1.0
C A:CAS470 5.0 37.8 1.0

Arsenic binding site 2 out of 2 in 4zt2

Go back to Arsenic Binding Sites List in 4zt2
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:53.7
occ:0.70
 AS B:CAS470 0.0 53.7 0.7
CE1 B:CAS470 2.0 53.3 0.7
CE2 B:CAS470 2.0 55.2 0.7
SG B:CAS470 2.2 46.3 1.0
CB B:CAS470 3.1 44.0 1.0
O B:ALA460 3.6 40.5 1.0
CA B:CAS470 3.6 42.3 1.0
CA B:PRO462 3.8 40.8 1.0
N B:PRO462 3.8 40.3 1.0
C B:ILE461 3.9 38.6 1.0
O B:ILE461 3.9 37.4 1.0
C B:ALA460 4.0 40.0 1.0
O B:HIS469 4.0 45.7 1.0
N B:CAS470 4.1 44.0 1.0
CG B:PRO462 4.3 43.3 1.0
C B:HIS469 4.3 45.7 1.0
CB B:ALA460 4.3 40.5 1.0
CD B:PRO462 4.4 41.8 1.0
CB B:ARG453 4.4 50.3 1.0
CB B:PRO462 4.4 42.2 1.0
N B:ILE461 4.5 38.8 1.0
CA B:ALA460 4.6 40.7 1.0
N B:ALA460 4.7 43.6 1.0
CA B:ILE461 4.7 38.8 1.0
CA B:ARG453 5.0 48.9 1.0

Reference:

Z.Zhang, C.Y.Koh, R.M.Ranade, S.Shibata, J.R.Gillespie, M.A.Hulverson, W.Huang, J.Nguyen, N.Pendem, M.H.Gelb, C.L.Verlinde, W.G.Hol, F.S.Buckner, E.Fan. 5-Fluoroimidazo[4,5-B]Pyridine Is A Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-Trna Synthetase Inhibitors. Acs Infect Dis. V. 2 399 2016.
ISSN: ESSN 2373-8227
PubMed: 27627628
DOI: 10.1021/ACSINFECDIS.6B00036
Page generated: Mon Jul 7 00:11:07 2025

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