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Arsenic 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
Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

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

Arsenic binding site 1 out of 2 in 4zt6

Go back to Arsenic Binding Sites List in 4zt6
Arsenic 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 Arsenic with other atoms in the As 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
A:As470

b:50.2
occ:0.70
 AS A:CAS470 0.0 50.2 0.7
CE2 A:CAS470 2.0 51.1 0.7
CE1 A:CAS470 2.0 49.5 0.7
SG A:CAS470 2.2 42.5 1.0
CB A:CAS470 3.0 38.5 1.0
CA A:CAS470 3.5 35.4 1.0
O A:ALA460 3.7 35.3 1.0
CA A:PRO462 3.8 34.2 1.0
N A:PRO462 3.8 33.8 1.0
O A:HIS469 3.9 35.7 1.0
C A:ILE461 4.0 33.7 1.0
O A:ILE461 4.0 33.2 1.0
N A:CAS470 4.0 35.1 1.0
C A:ALA460 4.1 34.7 1.0
C A:HIS469 4.2 35.1 1.0
CB A:ALA460 4.3 34.1 1.0
CG A:PRO462 4.3 36.3 1.0
CB A:PRO462 4.3 35.5 1.0
CB A:ARG453 4.4 43.0 1.0
CD A:PRO462 4.5 35.2 1.0
N A:ILE461 4.5 33.2 1.0
CA A:ALA460 4.6 35.2 1.0
CA A:ILE461 4.8 34.2 1.0
N A:ALA460 4.8 37.2 1.0
C A:CAS470 4.9 32.6 1.0
CA A:ARG453 5.0 42.1 1.0
O A:PRO467 5.0 42.6 1.0

Arsenic binding site 2 out of 2 in 4zt6

Go back to Arsenic Binding Sites List in 4zt6
Arsenic 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 Arsenic with other atoms in the As 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:As470

b:52.2
occ:0.70
 AS B:CAS470 0.0 52.2 0.7
CE2 B:CAS470 2.0 52.0 0.7
CE1 B:CAS470 2.0 51.1 0.7
SG B:CAS470 2.2 43.4 1.0
CB B:CAS470 3.1 39.5 1.0
CA B:CAS470 3.6 37.1 1.0
O B:ALA460 3.7 34.2 1.0
CA B:PRO462 3.7 36.4 1.0
N B:PRO462 3.8 36.1 1.0
O B:HIS469 3.9 36.5 1.0
C B:ILE461 3.9 34.6 1.0
O B:ILE461 4.0 34.3 1.0
C B:ALA460 4.1 34.2 1.0
N B:CAS470 4.1 36.8 1.0
C B:HIS469 4.3 37.1 1.0
CB B:ALA460 4.3 34.3 1.0
CG B:PRO462 4.3 37.9 1.0
CB B:PRO462 4.3 37.3 1.0
CB B:ARG453 4.4 39.7 1.0
CD B:PRO462 4.5 36.8 1.0
N B:ILE461 4.5 33.8 1.0
CA B:ALA460 4.6 34.3 1.0
CA B:ILE461 4.8 34.5 1.0
N B:ALA460 4.8 35.5 1.0
O B:PRO467 4.9 41.8 1.0
CA B:ARG453 4.9 38.3 1.0
C B:CAS470 5.0 34.8 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: Wed Jul 10 12:43:58 2024

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