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Chlorine 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
Arsenic (As) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 2 in 4zt4

Go back to Chlorine Binding Sites List in 4zt4
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:53.3
occ:1.00
 CL1 B:4RO803 0.0 53.3 1.0
C7 B:4RO803 1.8 60.0 1.0
C6 B:4RO803 2.7 57.3 1.0
C8 B:4RO803 2.7 60.3 1.0
N B:ILE248 3.5 34.7 1.0
OH B:TYR481 3.7 29.4 1.0
CG1 B:ILE248 3.8 36.5 1.0
CE1 B:HIS523 3.9 34.6 1.0
O B:ILE248 3.9 37.9 1.0
NE2 B:HIS523 4.0 34.5 1.0
CA B:PRO247 4.0 33.1 1.0
CB B:PRO247 4.0 34.0 1.0
C5 B:4RO803 4.0 57.1 1.0
C3 B:4RO803 4.0 63.0 1.0
C B:PRO247 4.3 34.4 1.0
CD1 B:ILE519 4.5 36.1 1.0
CA B:ILE248 4.5 35.4 1.0
CZ B:TYR481 4.5 29.5 1.0
C4 B:4RO803 4.5 58.9 1.0
C B:ILE248 4.6 36.2 1.0
CB B:ALA477 4.7 39.5 1.0
ND2 B:ASN480 4.8 33.5 1.0
CB B:ILE248 4.8 35.4 1.0
O B:HOH928 4.8 43.0 1.0
CD1 B:ILE248 4.9 37.2 1.0
O B:ALA477 5.0 41.5 1.0
CE2 B:TYR481 5.0 30.1 1.0

Chlorine binding site 2 out of 2 in 4zt4

Go back to Chlorine Binding Sites List in 4zt4
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl803

b:58.8
occ:1.00
 CL B:4RO803 0.0 58.8 1.0
C5 B:4RO803 1.7 57.1 1.0
C4 B:4RO803 2.7 58.9 1.0
C6 B:4RO803 2.7 57.3 1.0
CE3 B:TRP474 3.5 51.1 1.0
CZ3 B:TRP474 3.7 51.4 1.0
CB B:PHE522 3.9 40.4 1.0
CD2 B:PHE522 3.9 43.7 1.0
C7 B:4RO803 4.0 60.0 1.0
C3 B:4RO803 4.0 63.0 1.0
CG B:PHE522 4.0 42.0 1.0
CG2 B:VAL473 4.0 50.9 1.0
CG B:LEU478 4.1 37.9 1.0
O B:VAL473 4.2 45.5 1.0
CA B:TRP474 4.4 47.6 1.0
CD1 B:LEU478 4.4 38.7 1.0
C8 B:4RO803 4.5 60.3 1.0
C B:VAL473 4.6 46.9 1.0
CD2 B:LEU478 4.6 39.1 1.0
CB B:ALA477 4.6 39.5 1.0
CG1 B:VAL473 4.6 53.3 1.0
CD2 B:TRP474 4.7 51.1 1.0
CE2 B:PHE522 4.7 45.6 1.0
N B:TRP474 4.7 47.1 1.0
O B:TRP474 4.7 46.6 1.0
CB B:VAL473 4.9 51.0 1.0
CD1 B:PHE522 4.9 45.1 1.0
CH2 B:TRP474 5.0 53.1 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: Fri Jul 11 23:54:18 2025

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