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Chlorine 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
Arsenic (As) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 4zt3

Go back to Chlorine Binding Sites List in 4zt3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl806

b:51.0
occ:1.00
 CL1 B:4RQ806 0.0 51.0 1.0
C13 B:4RQ806 1.7 57.1 1.0
C14 B:4RQ806 2.7 58.6 1.0
C12 B:4RQ806 2.7 57.7 1.0
N B:ILE248 3.6 34.9 1.0
OH B:TYR481 3.6 33.5 1.0
CG1 B:ILE248 3.7 36.4 1.0
NE2 B:HIS523 3.9 38.0 1.0
O B:ILE248 3.9 38.3 1.0
CE1 B:HIS523 3.9 39.1 1.0
C11 B:4RQ806 4.0 58.2 1.0
C9 B:4RQ806 4.0 60.7 1.0
CA B:PRO247 4.1 33.9 1.0
CB B:PRO247 4.2 35.0 1.0
C B:PRO247 4.4 34.1 1.0
CZ B:TYR481 4.5 33.4 1.0
CA B:ILE248 4.5 35.7 1.0
C10 B:4RQ806 4.5 59.6 1.0
CB B:ALA477 4.6 45.0 1.0
C B:ILE248 4.6 37.5 1.0
O B:ALA477 4.7 42.5 1.0
CD1 B:ILE519 4.7 45.2 1.0
CB B:ILE248 4.7 35.8 1.0
CD1 B:ILE248 4.7 37.2 1.0
ND2 B:ASN480 4.8 37.5 1.0
C B:ALA477 4.8 42.8 1.0
O B:HOH922 4.9 36.6 1.0
CE2 B:TYR481 5.0 33.4 1.0

Chlorine binding site 2 out of 2 in 4zt3

Go back to Chlorine Binding Sites List in 4zt3
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl806

b:61.7
occ:1.00
 CL B:4RQ806 0.0 61.7 1.0
C11 B:4RQ806 1.7 58.2 1.0
C10 B:4RQ806 2.7 59.6 1.0
C12 B:4RQ806 2.7 57.7 1.0
CD2 B:PHE522 3.7 49.2 1.0
CE3 B:TRP474 3.7 57.4 1.0
CG2 B:VAL473 3.8 61.4 1.0
CG B:PHE522 3.9 48.0 1.0
CB B:PHE522 3.9 45.9 1.0
C13 B:4RQ806 4.0 57.1 1.0
C9 B:4RQ806 4.0 60.7 1.0
O B:VAL473 4.1 52.8 1.0
CZ3 B:TRP474 4.2 58.8 1.0
CA B:TRP474 4.3 52.9 1.0
CG B:LEU478 4.4 43.2 1.0
CE2 B:PHE522 4.4 51.3 1.0
CD1 B:LEU478 4.4 43.8 1.0
C B:VAL473 4.5 55.5 1.0
C14 B:4RQ806 4.5 58.6 1.0
N B:TRP474 4.7 54.6 1.0
CD2 B:TRP474 4.8 57.2 1.0
CG1 B:VAL473 4.8 62.8 1.0
CD1 B:PHE522 4.8 49.5 1.0
CB B:VAL473 4.8 62.2 1.0
CD2 B:LEU478 4.9 43.3 1.0
CB B:ALA477 4.9 45.0 1.0
CB B:TRP474 5.0 53.5 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: Fri Jul 11 23:54:16 2025

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