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Arsenic in PDB 4zt4: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708), PDB code: 4zt4 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) 38.59 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.516, 106.128, 207.106, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.5

Other elements in 4zt4:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) (pdb code 4zt4). 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 Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708), PDB code: 4zt4:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4zt4

Go back to Arsenic Binding Sites List in 4zt4
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)


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 Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:55.4
occ:0.70
 AS A:CAS470 0.0 55.4 0.7
CE2 A:CAS470 2.0 56.0 0.7
CE1 A:CAS470 2.0 54.2 0.7
SG A:CAS470 2.2 48.4 1.0
CB A:CAS470 3.1 42.6 1.0
CA A:CAS470 3.5 38.4 1.0
O A:ALA460 3.7 38.0 1.0
N A:PRO462 3.8 37.2 1.0
CA A:PRO462 3.8 38.2 1.0
C A:ILE461 3.9 36.0 1.0
O A:ILE461 4.0 34.4 1.0
O A:HIS469 4.0 39.3 1.0
C A:ALA460 4.0 37.3 1.0
N A:CAS470 4.1 38.0 1.0
C A:HIS469 4.3 38.4 1.0
CG A:PRO462 4.3 40.6 1.0
CD A:PRO462 4.4 39.3 1.0
CB A:ALA460 4.4 36.0 1.0
CB A:ARG453 4.4 46.0 1.0
CB A:PRO462 4.4 39.5 1.0
N A:ILE461 4.5 35.4 1.0
CA A:ALA460 4.6 37.3 1.0
CA A:ILE461 4.7 35.9 1.0
N A:ALA460 4.8 39.4 1.0
C A:CAS470 4.9 35.4 1.0
CA A:ASN458 5.0 47.6 1.0
O A:PRO467 5.0 45.9 1.0
CA A:ARG453 5.0 44.8 1.0

Arsenic binding site 2 out of 2 in 4zt4

Go back to Arsenic Binding Sites List in 4zt4
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)


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 Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:62.7
occ:0.70
 AS B:CAS470 0.0 62.7 0.7
CE1 B:CAS470 2.0 60.5 0.7
CE2 B:CAS470 2.0 61.9 0.7
SG B:CAS470 2.2 51.3 1.0
CB B:CAS470 3.1 48.6 1.0
CA B:CAS470 3.6 46.6 1.0
O B:ALA460 3.7 41.9 1.0
CA B:PRO462 3.8 44.5 1.0
N B:PRO462 3.9 43.5 1.0
C B:ILE461 3.9 42.5 1.0
O B:ILE461 3.9 42.4 1.0
O B:HIS469 4.0 47.3 1.0
C B:ALA460 4.0 42.5 1.0
N B:CAS470 4.1 47.1 1.0
C B:HIS469 4.3 48.0 1.0
CG B:PRO462 4.3 45.5 1.0
CD B:PRO462 4.4 44.6 1.0
CB B:ALA460 4.4 42.4 1.0
CB B:PRO462 4.4 45.2 1.0
CB B:ARG453 4.4 51.1 1.0
N B:ILE461 4.5 42.6 1.0
CA B:ALA460 4.7 42.6 1.0
O B:HOH991 4.7 56.9 1.0
CA B:ILE461 4.7 42.8 1.0
N B:ALA460 4.8 44.3 1.0
C B:CAS470 4.9 44.4 1.0
O B:PRO467 5.0 53.5 1.0
CA B:ARG453 5.0 51.3 1.0
CA B:ASN458 5.0 56.3 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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