Atomistry » Arsenic » PDB 4zt2-5hr7 » 4zt4
Atomistry »
  Arsenic »
    PDB 4zt2-5hr7 »
      4zt4 »

Arsenic in PDB 4zt4: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708), PDB code: 4zt4 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) 38.59 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.516, 106.128, 207.106, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.5

Other elements in 4zt4:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) (pdb code 4zt4). 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 Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708), PDB code: 4zt4:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4zt4

Go back to Arsenic Binding Sites List in 4zt4
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)


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 Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:55.4
occ:0.70
 AS A:CAS470 0.0 55.4 0.7
CE2 A:CAS470 2.0 56.0 0.7
CE1 A:CAS470 2.0 54.2 0.7
SG A:CAS470 2.2 48.4 1.0
CB A:CAS470 3.1 42.6 1.0
CA A:CAS470 3.5 38.4 1.0
O A:ALA460 3.7 38.0 1.0
N A:PRO462 3.8 37.2 1.0
CA A:PRO462 3.8 38.2 1.0
C A:ILE461 3.9 36.0 1.0
O A:ILE461 4.0 34.4 1.0
O A:HIS469 4.0 39.3 1.0
C A:ALA460 4.0 37.3 1.0
N A:CAS470 4.1 38.0 1.0
C A:HIS469 4.3 38.4 1.0
CG A:PRO462 4.3 40.6 1.0
CD A:PRO462 4.4 39.3 1.0
CB A:ALA460 4.4 36.0 1.0
CB A:ARG453 4.4 46.0 1.0
CB A:PRO462 4.4 39.5 1.0
N A:ILE461 4.5 35.4 1.0
CA A:ALA460 4.6 37.3 1.0
CA A:ILE461 4.7 35.9 1.0
N A:ALA460 4.8 39.4 1.0
C A:CAS470 4.9 35.4 1.0
CA A:ASN458 5.0 47.6 1.0
O A:PRO467 5.0 45.9 1.0
CA A:ARG453 5.0 44.8 1.0

Arsenic binding site 2 out of 2 in 4zt4

Go back to Arsenic Binding Sites List in 4zt4
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708)


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 Inhibitorn-(3,5-Dichlorobenzyl)-2,2-Difluoro-N'-(1H-Imidazo[4,5- B]Pyridin-2-Yl)Propane-1,3-Diamine (Chem 1708) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:62.7
occ:0.70
 AS B:CAS470 0.0 62.7 0.7
CE1 B:CAS470 2.0 60.5 0.7
CE2 B:CAS470 2.0 61.9 0.7
SG B:CAS470 2.2 51.3 1.0
CB B:CAS470 3.1 48.6 1.0
CA B:CAS470 3.6 46.6 1.0
O B:ALA460 3.7 41.9 1.0
CA B:PRO462 3.8 44.5 1.0
N B:PRO462 3.9 43.5 1.0
C B:ILE461 3.9 42.5 1.0
O B:ILE461 3.9 42.4 1.0
O B:HIS469 4.0 47.3 1.0
C B:ALA460 4.0 42.5 1.0
N B:CAS470 4.1 47.1 1.0
C B:HIS469 4.3 48.0 1.0
CG B:PRO462 4.3 45.5 1.0
CD B:PRO462 4.4 44.6 1.0
CB B:ALA460 4.4 42.4 1.0
CB B:PRO462 4.4 45.2 1.0
CB B:ARG453 4.4 51.1 1.0
N B:ILE461 4.5 42.6 1.0
CA B:ALA460 4.7 42.6 1.0
O B:HOH991 4.7 56.9 1.0
CA B:ILE461 4.7 42.8 1.0
N B:ALA460 4.8 44.3 1.0
C B:CAS470 4.9 44.4 1.0
O B:PRO467 5.0 53.5 1.0
CA B:ARG453 5.0 51.3 1.0
CA B:ASN458 5.0 56.3 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 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy