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Chlorine in PDB 4zt5: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655), PDB code: 4zt5 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) 38.67 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.794, 106.021, 207.659, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.9

Other elements in 4zt5:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655) also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655) (pdb code 4zt5). 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 (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655), PDB code: 4zt5:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4zt5

Go back to Chlorine Binding Sites List in 4zt5
Chlorine binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655)


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 (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl806

b:58.3
occ:1.00
 CL1 B:4RN806 0.0 58.3 1.0
C8 B:4RN806 1.7 51.5 1.0
C9 B:4RN806 2.7 51.6 1.0
C7 B:4RN806 2.7 50.4 1.0
CE3 B:TRP474 3.4 40.9 1.0
CZ3 B:TRP474 3.6 42.1 1.0
CB B:PHE522 3.8 41.2 1.0
CD2 B:PHE522 3.8 43.7 1.0
CG B:PHE522 4.0 42.1 1.0
C6 B:4RN806 4.0 53.2 1.0
C4 B:4RN806 4.0 53.5 1.0
CG B:LEU478 4.0 41.0 1.0
CG2 B:VAL473 4.2 44.5 1.0
CD1 B:LEU478 4.3 41.3 1.0
CD2 B:LEU478 4.3 44.1 1.0
C5 B:4RN806 4.5 52.4 1.0
O B:VAL473 4.5 40.0 1.0
CA B:TRP474 4.5 40.9 1.0
CD2 B:TRP474 4.6 41.4 1.0
CE2 B:PHE522 4.7 44.9 1.0
CG1 B:VAL473 4.8 44.9 1.0
C B:VAL473 4.8 41.3 1.0
CB B:ALA477 4.8 42.2 1.0
CH2 B:TRP474 4.8 44.3 1.0
O B:TRP474 4.9 40.5 1.0
CD1 B:PHE522 4.9 43.0 1.0
N B:TRP474 4.9 40.7 1.0

Chlorine binding site 2 out of 2 in 4zt5

Go back to Chlorine Binding Sites List in 4zt5
Chlorine binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655)


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 (2S)-N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)-2- Methylpropane-1,3-Diamine (Chem 1655) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl806

b:50.8
occ:1.00
 CL B:4RN806 0.0 50.8 1.0
C6 B:4RN806 1.8 53.2 1.0
C7 B:4RN806 2.7 50.4 1.0
C5 B:4RN806 2.7 52.4 1.0
OH B:TYR481 3.5 32.2 1.0
N B:ILE248 3.6 37.4 1.0
NE2 B:HIS523 3.7 36.8 1.0
CG1 B:ILE248 3.8 40.1 1.0
CE1 B:HIS523 3.8 39.3 1.0
C8 B:4RN806 4.0 51.5 1.0
CA B:PRO247 4.0 36.8 1.0
C4 B:4RN806 4.0 53.5 1.0
O B:ILE248 4.1 42.0 1.0
CB B:PRO247 4.2 39.0 1.0
CZ B:TYR481 4.3 32.8 1.0
C B:PRO247 4.3 37.9 1.0
C9 B:4RN806 4.5 51.6 1.0
ND2 B:ASN480 4.6 35.4 1.0
CA B:ILE248 4.6 37.7 1.0
CB B:ALA477 4.6 42.2 1.0
O B:ALA477 4.7 43.7 1.0
CD1 B:ILE519 4.7 42.5 1.0
CE2 B:TYR481 4.7 33.3 1.0
CB B:ILE248 4.8 38.0 1.0
CD1 B:ILE248 4.8 41.7 1.0
CD2 B:LEU478 4.8 44.1 1.0
C B:ALA477 4.8 40.9 1.0
C B:ILE248 4.8 39.2 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 23:54:47 2025

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