Atomistry » Arsenic » PDB 4zt2-5hr7 » 4zt3
Atomistry »
  Arsenic »
    PDB 4zt2-5hr7 »
      4zt3 »

Arsenic in PDB 4zt3: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614), PDB code: 4zt3 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) 38.64 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.696, 106.054, 207.453, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.9

Other elements in 4zt3:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) 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-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) (pdb code 4zt3). 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-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614), PDB code: 4zt3:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4zt3

Go back to Arsenic Binding Sites List in 4zt3
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)


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-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:63.2
occ:0.70
 AS A:CAS470 0.0 63.2 0.7
CE2 A:CAS470 2.0 64.8 0.7
CE1 A:CAS470 2.0 64.7 0.7
SG A:CAS470 2.2 56.0 1.0
CB A:CAS470 3.1 48.2 1.0
CA A:CAS470 3.6 44.4 1.0
O A:ALA460 3.7 40.6 1.0
O A:HIS469 3.9 44.4 1.0
CA A:PRO462 4.0 38.9 1.0
N A:CAS470 4.0 43.6 1.0
N A:PRO462 4.0 38.2 1.0
C A:ALA460 4.2 38.7 1.0
C A:HIS469 4.2 43.6 1.0
C A:ILE461 4.2 36.0 1.0
CB A:ARG453 4.2 55.3 1.0
O A:ILE461 4.2 34.4 1.0
CG A:PRO462 4.4 43.0 1.0
CD A:PRO462 4.5 40.8 1.0
CB A:ALA460 4.6 38.0 1.0
CB A:PRO462 4.6 41.7 1.0
N A:ILE461 4.7 36.2 1.0
CA A:ALA460 4.8 39.4 1.0
CA A:ARG453 4.8 52.5 1.0
O A:PRO467 4.9 51.0 1.0
N A:ALA460 4.9 43.1 1.0
CA A:ASN458 4.9 54.7 1.0
OD1 A:ASN458 5.0 58.1 1.0
C A:CAS470 5.0 40.9 1.0
CA A:ILE461 5.0 36.1 1.0
C A:ASN458 5.0 52.9 1.0

Arsenic binding site 2 out of 2 in 4zt3

Go back to Arsenic Binding Sites List in 4zt3
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor N-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614)


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-(3,5-Dichlorobenzyl)-N'-(5-Fluoro-1H-Imidazo[4,5-B]Pyridin-2-Yl) Propane-1,3-Diamine (Chem 1614) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:77.3
occ:0.70
 AS B:CAS470 0.0 77.3 0.7
CE2 B:CAS470 2.0 77.5 0.7
CE1 B:CAS470 2.0 78.2 0.7
SG B:CAS470 2.2 70.8 1.0
CB B:CAS470 3.1 64.7 1.0
CA B:CAS470 3.7 61.1 1.0
O B:ALA460 3.7 53.2 1.0
O B:HIS469 3.9 60.2 1.0
CA B:PRO462 4.0 51.7 1.0
N B:CAS470 4.1 61.3 1.0
N B:PRO462 4.1 51.0 1.0
CB B:ARG453 4.2 70.2 1.0
C B:HIS469 4.2 61.1 1.0
C B:ALA460 4.2 52.0 1.0
C B:ILE461 4.2 49.5 1.0
O B:ILE461 4.2 48.4 1.0
CG B:PRO462 4.4 54.6 1.0
CB B:ALA460 4.6 52.6 1.0
CD B:PRO462 4.6 52.7 1.0
CB B:PRO462 4.6 53.6 1.0
N B:ILE461 4.8 49.9 1.0
CA B:ALA460 4.8 53.0 1.0
CA B:ARG453 4.8 69.5 1.0
O B:PRO467 4.8 65.6 1.0
CA B:ASN458 4.9 68.1 1.0
N B:ALA460 4.9 56.2 1.0
OD1 B:ASN458 5.0 72.0 1.0
C B:ASN458 5.0 65.5 1.0
O B:ASN458 5.0 65.0 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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy