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Chlorine in PDB 4zt2: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575), PDB code: 4zt2 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) 35.35 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.068, 106.070, 207.674, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.8

Other elements in 4zt2:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) 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 N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) (pdb code 4zt2). 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'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575), PDB code: 4zt2:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4zt2

Go back to Chlorine Binding Sites List in 4zt2
Chlorine binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)


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'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:42.3
occ:1.00
 CL1 B:4RP801 0.0 42.3 1.0
C2 B:4RP801 1.7 40.0 1.0
C3 B:4RP801 2.7 39.5 1.0
C1 B:4RP801 2.7 42.1 1.0
CE3 B:TRP474 3.4 36.3 1.0
CB B:PHE522 3.7 37.9 1.0
CZ3 B:TRP474 3.8 36.9 1.0
CD2 B:PHE522 3.8 38.3 1.0
CG B:PHE522 3.9 37.9 1.0
CG B:LEU478 3.9 35.3 1.0
C B:4RP801 4.0 42.5 1.0
C4 B:4RP801 4.0 40.0 1.0
CD1 B:LEU478 4.1 35.4 1.0
CG2 B:VAL473 4.3 41.5 1.0
O B:VAL473 4.3 37.3 1.0
CD2 B:LEU478 4.3 35.9 1.0
CA B:TRP474 4.4 37.2 1.0
C15 B:4RP801 4.5 39.9 1.0
CD2 B:TRP474 4.5 36.9 1.0
CE2 B:PHE522 4.7 39.1 1.0
C B:VAL473 4.7 38.2 1.0
CG1 B:VAL473 4.8 42.6 1.0
N B:TRP474 4.8 37.4 1.0
CB B:ALA477 4.8 39.2 1.0
CD1 B:PHE522 4.9 38.8 1.0
CB B:TRP474 4.9 36.6 1.0

Chlorine binding site 2 out of 2 in 4zt2

Go back to Chlorine Binding Sites List in 4zt2
Chlorine binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575)


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'-(1H-Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3- Diamine (Chem 1575) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:47.3
occ:1.00
 CL B:4RP801 0.0 47.3 1.0
C B:4RP801 1.7 42.5 1.0
C1 B:4RP801 2.7 42.1 1.0
C15 B:4RP801 2.7 39.9 1.0
OH B:TYR481 3.6 30.0 1.0
N B:ILE248 3.6 34.7 1.0
CE1 B:HIS523 3.8 33.8 1.0
NE2 B:HIS523 3.8 33.3 1.0
CG1 B:ILE248 3.8 34.9 1.0
C2 B:4RP801 4.0 40.0 1.0
C4 B:4RP801 4.0 40.0 1.0
CA B:PRO247 4.0 34.8 1.0
CB B:PRO247 4.1 35.9 1.0
O B:ILE248 4.1 32.9 1.0
CZ B:TYR481 4.3 30.4 1.0
C B:PRO247 4.4 35.1 1.0
C3 B:4RP801 4.5 39.5 1.0
CD1 B:ILE519 4.6 42.8 1.0
ND2 B:ASN480 4.6 34.3 1.0
CA B:ILE248 4.6 33.4 1.0
O B:ALA477 4.6 36.8 1.0
CB B:ALA477 4.7 39.2 1.0
CE2 B:TYR481 4.8 30.5 1.0
CD1 B:ILE248 4.8 36.0 1.0
CB B:ILE248 4.8 33.4 1.0
C B:ILE248 4.8 33.3 1.0
C B:ALA477 4.8 36.2 1.0
CD2 B:LEU478 4.8 35.9 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 26 04:49:33 2024

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