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Arsenic 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:

Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

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

Arsenic binding site 1 out of 2 in 4zt5

Go back to Arsenic Binding Sites List in 4zt5
Arsenic 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 Arsenic with other atoms in the As 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
A:As470

b:76.3
occ:0.70
 AS A:CAS470 0.0 76.3 0.7
CE2 A:CAS470 2.0 76.6 0.7
CE1 A:CAS470 2.0 74.3 0.7
SG A:CAS470 2.2 61.8 1.0
CB A:CAS470 3.0 53.2 1.0
CA A:CAS470 3.5 47.2 1.0
O A:HIS469 3.9 46.2 1.0
CA A:PRO462 3.9 43.2 1.0
O A:ALA460 3.9 43.4 1.0
N A:CAS470 4.0 46.5 1.0
N A:PRO462 4.0 42.6 1.0
C A:ILE461 4.1 40.7 1.0
O A:ILE461 4.1 38.9 1.0
C A:HIS469 4.1 45.5 1.0
CB A:ARG453 4.2 57.9 1.0
C A:ALA460 4.2 41.5 1.0
CB A:ALA460 4.4 42.2 1.0
CB A:PRO462 4.5 45.4 1.0
CG A:PRO462 4.6 46.7 1.0
N A:ILE461 4.7 39.6 1.0
CD A:PRO462 4.7 45.0 1.0
CA A:ALA460 4.7 43.1 1.0
CA A:ARG453 4.8 55.1 1.0
CA A:ASN458 4.8 56.5 1.0
N A:ALA460 4.8 45.8 1.0
C A:ASN458 4.9 55.1 1.0
O A:ASN458 4.9 55.5 1.0
O A:PRO467 4.9 56.1 1.0
CA A:ILE461 4.9 41.0 1.0
C A:CAS470 4.9 43.0 1.0

Arsenic binding site 2 out of 2 in 4zt5

Go back to Arsenic Binding Sites List in 4zt5
Arsenic 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 Arsenic with other atoms in the As 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:As470

b:83.1
occ:0.70
 AS B:CAS470 0.0 83.1 0.7
CE2 B:CAS470 2.0 77.1 0.7
CE1 B:CAS470 2.0 78.5 0.7
SG B:CAS470 2.2 65.0 1.0
CB B:CAS470 3.3 57.5 1.0
CB B:ARG453 3.8 54.8 1.0
CA B:CAS470 4.0 52.5 1.0
O B:ALA460 4.2 48.9 1.0
O B:HIS469 4.3 48.5 1.0
N B:CAS470 4.3 51.8 1.0
CA B:ARG453 4.4 53.3 1.0
CA B:ASN458 4.4 57.1 1.0
CA B:PRO462 4.4 48.2 1.0
C B:HIS469 4.4 52.1 1.0
C B:ALA460 4.5 47.5 1.0
CB B:ALA460 4.5 47.1 1.0
C B:ASN458 4.5 54.7 1.0
N B:PRO462 4.6 48.1 1.0
O B:ASN458 4.6 56.1 1.0
C B:ILE461 4.7 46.6 1.0
O B:ILE461 4.7 46.0 1.0
N B:ALA460 4.7 47.4 1.0
CA B:ALA460 4.8 46.8 1.0
O B:PRO467 4.9 61.3 1.0
CB B:PRO462 4.9 49.8 1.0
CG B:PRO462 4.9 50.8 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 12:43:57 2024

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