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Fluorine 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:

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 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 Fluorine atom.
In total 2 binding sites of Fluorine 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 Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4zt4

Go back to Fluorine Binding Sites List in 4zt4
Fluorine 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 Fluorine with other atoms in the F 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
B:F803

b:63.5
occ:1.00
 F B:4RO803 0.0 63.5 1.0
C B:4RO803 1.4 64.3 1.0
F1 B:4RO803 2.2 61.4 1.0
C9 B:4RO803 2.4 64.4 1.0
C1 B:4RO803 2.5 62.9 1.0
N B:4RO803 2.9 64.4 1.0
N1 B:4RO803 3.7 63.5 1.0
O B:HOH1105 3.9 54.2 1.0
C2 B:4RO803 4.3 62.8 1.0
C10 B:4RO803 4.7 62.0 1.0
CD2 B:TYR250 4.8 55.5 1.0
N2 B:4RO803 4.9 60.1 1.0
CE2 B:TYR250 4.9 56.5 1.0
CG B:TYR250 5.0 54.7 1.0

Fluorine binding site 2 out of 2 in 4zt4

Go back to Fluorine Binding Sites List in 4zt4
Fluorine 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 Fluorine with other atoms in the F 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:F803

b:61.4
occ:1.00
 F1 B:4RO803 0.0 61.4 1.0
C B:4RO803 1.4 64.3 1.0
F B:4RO803 2.2 63.5 1.0
C9 B:4RO803 2.4 64.4 1.0
C1 B:4RO803 2.5 62.9 1.0
N1 B:4RO803 3.0 63.5 1.0
N B:4RO803 3.1 64.4 1.0
O B:HOH1105 3.2 54.2 1.0
CG2 B:VAL473 3.5 50.9 1.0
C10 B:4RO803 3.6 62.0 1.0
N2 B:4RO803 3.8 60.1 1.0
CG1 B:VAL473 3.9 53.3 1.0
CB B:VAL473 4.0 51.0 1.0
C2 B:4RO803 4.4 62.8 1.0
C4 B:4RO803 4.4 58.9 1.0
N4 B:4RO803 4.6 61.5 1.0
C3 B:4RO803 4.8 63.0 1.0
C11 B:4RO803 5.0 58.8 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 02:02:27 2025

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