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Arsenic in PDB 4zt3: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614), PDB code: 4zt3 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) 38.64 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.696, 106.054, 207.453, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.9

Other elements in 4zt3:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) also contains other interesting chemical elements:

Fluorine (F) 1 atom
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'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) (pdb code 4zt3). 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'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614), PDB code: 4zt3:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4zt3

Go back to Arsenic Binding Sites List in 4zt3
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)


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'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:63.2
occ:0.70
 AS A:CAS470 0.0 63.2 0.7
CE2 A:CAS470 2.0 64.8 0.7
CE1 A:CAS470 2.0 64.7 0.7
SG A:CAS470 2.2 56.0 1.0
CB A:CAS470 3.1 48.2 1.0
CA A:CAS470 3.6 44.4 1.0
O A:ALA460 3.7 40.6 1.0
O A:HIS469 3.9 44.4 1.0
CA A:PRO462 4.0 38.9 1.0
N A:CAS470 4.0 43.6 1.0
N A:PRO462 4.0 38.2 1.0
C A:ALA460 4.2 38.7 1.0
C A:HIS469 4.2 43.6 1.0
C A:ILE461 4.2 36.0 1.0
CB A:ARG453 4.2 55.3 1.0
O A:ILE461 4.2 34.4 1.0
CG A:PRO462 4.4 43.0 1.0
CD A:PRO462 4.5 40.8 1.0
CB A:ALA460 4.6 38.0 1.0
CB A:PRO462 4.6 41.7 1.0
N A:ILE461 4.7 36.2 1.0
CA A:ALA460 4.8 39.4 1.0
CA A:ARG453 4.8 52.5 1.0
O A:PRO467 4.9 51.0 1.0
N A:ALA460 4.9 43.1 1.0
CA A:ASN458 4.9 54.7 1.0
OD1 A:ASN458 5.0 58.1 1.0
C A:CAS470 5.0 40.9 1.0
CA A:ILE461 5.0 36.1 1.0
C A:ASN458 5.0 52.9 1.0

Arsenic binding site 2 out of 2 in 4zt3

Go back to Arsenic Binding Sites List in 4zt3
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)


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'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:77.3
occ:0.70
 AS B:CAS470 0.0 77.3 0.7
CE2 B:CAS470 2.0 77.5 0.7
CE1 B:CAS470 2.0 78.2 0.7
SG B:CAS470 2.2 70.8 1.0
CB B:CAS470 3.1 64.7 1.0
CA B:CAS470 3.7 61.1 1.0
O B:ALA460 3.7 53.2 1.0
O B:HIS469 3.9 60.2 1.0
CA B:PRO462 4.0 51.7 1.0
N B:CAS470 4.1 61.3 1.0
N B:PRO462 4.1 51.0 1.0
CB B:ARG453 4.2 70.2 1.0
C B:HIS469 4.2 61.1 1.0
C B:ALA460 4.2 52.0 1.0
C B:ILE461 4.2 49.5 1.0
O B:ILE461 4.2 48.4 1.0
CG B:PRO462 4.4 54.6 1.0
CB B:ALA460 4.6 52.6 1.0
CD B:PRO462 4.6 52.7 1.0
CB B:PRO462 4.6 53.6 1.0
N B:ILE461 4.8 49.9 1.0
CA B:ALA460 4.8 53.0 1.0
CA B:ARG453 4.8 69.5 1.0
O B:PRO467 4.8 65.6 1.0
CA B:ASN458 4.9 68.1 1.0
N B:ALA460 4.9 56.2 1.0
OD1 B:ASN458 5.0 72.0 1.0
C B:ASN458 5.0 65.5 1.0
O B:ASN458 5.0 65.0 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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