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Chlorine in PDB 4zt6: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709), PDB code: 4zt6 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) 37.87 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.077, 106.229, 206.561, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.3

Other elements in 4zt6:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709) 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-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709) (pdb code 4zt6). 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-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709), PDB code: 4zt6:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4zt6

Go back to Chlorine Binding Sites List in 4zt6
Chlorine binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709)


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-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:37.9
occ:1.00
 CL1 B:4RD802 0.0 37.9 1.0
C14 B:4RD802 1.7 37.8 1.0
C13 B:4RD802 2.7 38.7 1.0
C15 B:4RD802 2.7 37.9 1.0
CE3 B:TRP474 3.6 30.7 1.0
CZ3 B:TRP474 3.6 31.9 1.0
CD2 B:PHE522 3.7 31.3 1.0
CB B:PHE522 3.9 30.7 1.0
CG B:PHE522 4.0 30.7 1.0
C12 B:4RD802 4.0 40.4 1.0
C16 B:4RD802 4.0 38.8 1.0
CG2 B:VAL473 4.0 36.3 1.0
CG B:LEU478 4.2 32.1 1.0
CD1 B:LEU478 4.4 32.5 1.0
CE2 B:PHE522 4.5 32.3 1.0
C11 B:4RD802 4.5 38.9 1.0
CD2 B:LEU478 4.6 33.5 1.0
O B:VAL473 4.7 33.5 1.0
CG1 B:VAL473 4.7 36.9 1.0
CB B:ALA477 4.7 30.9 1.0
CA B:TRP474 4.8 31.9 1.0
CD2 B:TRP474 4.8 31.4 1.0
CH2 B:TRP474 4.9 32.5 1.0
C B:VAL473 4.9 33.6 1.0
CD1 B:PHE522 4.9 31.5 1.0
CB B:VAL473 5.0 36.1 1.0

Chlorine binding site 2 out of 2 in 4zt6

Go back to Chlorine Binding Sites List in 4zt6
Chlorine binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709)


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-[(4R)-6,8-Dichloro-3,4-Dihydro-2H-Chromen-4-Yl]-N'-(5-Fluoro-1H- Imidazo[4,5-B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1709) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:47.7
occ:1.00
 CL B:4RD802 0.0 47.7 1.0
C12 B:4RD802 1.7 40.4 1.0
C13 B:4RD802 2.7 38.7 1.0
C11 B:4RD802 2.7 38.9 1.0
O B:4RD802 3.0 37.7 1.0
OH B:TYR481 3.5 23.9 1.0
N B:ILE248 3.5 27.4 1.0
NE2 B:HIS523 3.7 28.6 1.0
CE1 B:HIS523 3.7 29.9 1.0
CA B:PRO247 3.8 27.0 1.0
CB B:PRO247 3.9 27.4 1.0
CG1 B:ILE248 3.9 27.4 1.0
C14 B:4RD802 4.0 37.8 1.0
C16 B:4RD802 4.0 38.8 1.0
C B:PRO247 4.2 27.6 1.0
O B:ILE248 4.2 31.0 1.0
CZ B:TYR481 4.3 24.5 1.0
C10 B:4RD802 4.4 37.6 1.0
CD1 B:ILE519 4.5 28.7 1.0
C15 B:4RD802 4.5 37.9 1.0
CA B:ILE248 4.5 27.6 1.0
ND2 B:ASN480 4.6 29.6 1.0
CE2 B:TYR481 4.7 24.7 1.0
CB B:ILE248 4.8 27.4 1.0
C B:ILE248 4.8 29.3 1.0
CB B:ALA477 4.9 30.9 1.0
O B:ALA477 4.9 32.8 1.0
CD2 B:LEU478 5.0 33.5 1.0
CD1 B:ILE248 5.0 28.1 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 23:54:49 2025

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