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Fluorine 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:

Arsenic (As) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total only one binding site of Fluorine was 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:

Fluorine binding site 1 out of 1 in 4zt3

Go back to Fluorine Binding Sites List in 4zt3
Fluorine binding site 1 out of 1 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 Fluorine with other atoms in the F 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
B:F806

b:50.4
occ:1.00
 F B:4RQ806 0.0 50.4 1.0
C B:4RQ806 1.4 54.7 1.0
N4 B:4RQ806 2.3 58.0 1.0
C1 B:4RQ806 2.3 54.8 1.0
CD2 B:LEU456 2.9 65.9 1.0
CD1 B:TYR472 3.3 62.8 1.0
C15 B:4RQ806 3.5 61.9 1.0
C2 B:4RQ806 3.6 55.3 1.0
CE1 B:TYR472 3.6 64.1 1.0
CA B:GLY290 3.8 49.8 1.0
CD1 B:LEU456 3.9 64.7 1.0
CG B:LEU456 4.0 66.8 1.0
C3 B:4RQ806 4.1 60.7 1.0
N B:VAL473 4.1 58.9 1.0
CA B:TYR472 4.2 58.0 1.0
O B:VAL471 4.3 54.7 1.0
O B:HOH960 4.4 44.0 1.0
CG B:TYR472 4.4 61.4 1.0
C B:TYR472 4.4 57.0 1.0
N B:GLY290 4.5 47.9 1.0
CB B:ALA460 4.6 52.6 1.0
N B:GLN291 4.7 56.0 1.0
N3 B:4RQ806 4.8 63.2 1.0
C B:GLY290 4.8 52.6 1.0
OE2 B:GLU368 4.8 0.6 1.0
CB B:TYR472 4.9 59.5 1.0
CZ B:TYR472 4.9 64.3 1.0
CA B:VAL473 4.9 59.3 1.0
CB B:LEU456 4.9 68.1 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: Tue Jul 15 02:02:13 2025

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