Atomistry » Arsenic » PDB 4mwd-4uha » 4mwe
Atomistry »
  Arsenic »
    PDB 4mwd-4uha »
      4mwe »

Arsenic in PDB 4mwe: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475), PDB code: 4mwe was solved by C.Y.Koh, J.E.Kim, A.B.Wetzel, W.J.De Van Der Schueren, S.Shibata, J.Liu, Z.Zhang, E.Fan, C.L.M.J.Verlinde, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.448, 106.086, 206.505, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.1

Other elements in 4mwe:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475) (pdb code 4mwe). 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 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475), PDB code: 4mwe:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4mwe

Go back to Arsenic Binding Sites List in 4mwe
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475)


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 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:48.1
occ:0.70
 AS A:CAS470 0.0 48.1 0.7
CE2 A:CAS470 2.0 49.5 0.7
CE1 A:CAS470 2.0 48.2 0.7
SG A:CAS470 2.2 46.3 1.0
CB A:CAS470 3.2 41.4 1.0
CA A:CAS470 3.6 39.1 1.0
O A:ALA460 3.7 37.4 1.0
N A:PRO462 3.8 33.6 1.0
CA A:PRO462 3.8 34.4 1.0
O A:HIS469 3.9 40.2 1.0
C A:ALA460 3.9 36.1 1.0
C A:ILE461 4.0 33.3 1.0
O A:ILE461 4.1 32.7 1.0
N A:CAS470 4.1 38.6 1.0
CB A:ALA460 4.2 36.2 1.0
C A:HIS469 4.3 39.9 1.0
CG A:PRO462 4.4 34.9 1.0
N A:ILE461 4.4 34.4 1.0
CD A:PRO462 4.4 34.0 1.0
CB A:PRO462 4.4 34.5 1.0
CA A:ALA460 4.5 36.7 1.0
CB A:ARG453 4.5 44.7 1.0
N A:ALA460 4.6 39.3 1.0
CA A:ILE461 4.7 33.9 1.0
C A:CAS470 4.9 36.6 1.0

Arsenic binding site 2 out of 2 in 4mwe

Go back to Arsenic Binding Sites List in 4mwe
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475)


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 1-(3-{[5-Chloro-3-(Prop-2-En-1-Yl)-2-(Prop-2-En-1-Yloxy) Benzyl]Amino}Propyl)-3-Thiophen-3-Ylurea (Chem 1475) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:50.9
occ:0.70
 AS B:CAS470 0.0 50.9 0.7
CE1 B:CAS470 1.9 49.1 0.7
CE2 B:CAS470 2.0 52.6 0.7
SG B:CAS470 2.2 47.6 1.0
CB B:CAS470 3.2 43.9 1.0
CA B:CAS470 3.8 41.2 1.0
O B:ALA460 3.9 36.2 1.0
CB B:ARG453 4.1 46.4 1.0
O B:ILE461 4.2 37.1 1.0
C B:ALA460 4.2 38.1 1.0
O B:HIS469 4.2 40.0 1.0
N B:CAS470 4.2 40.9 1.0
C B:ILE461 4.3 37.7 1.0
CA B:PRO462 4.3 39.1 1.0
CB B:ALA460 4.3 39.2 1.0
N B:PRO462 4.3 39.3 1.0
C B:HIS469 4.4 42.4 1.0
CA B:ARG453 4.6 45.8 1.0
CA B:ALA460 4.6 38.9 1.0
CB B:PRO462 4.7 39.8 1.0
N B:ILE461 4.7 38.4 1.0
CG B:PRO462 4.7 40.4 1.0
N B:ALA460 4.7 40.1 1.0
CD B:PRO462 4.9 39.9 1.0
CA B:ASN458 5.0 45.0 1.0
O B:HOH921 5.0 45.6 1.0
CA B:ILE461 5.0 38.2 1.0

Reference:

C.Y.Koh, J.E.Kim, A.B.Wetzel, W.J.De Van Der Schueren, S.Shibata, R.M.Ranade, J.Liu, Z.Zhang, J.R.Gillespie, F.S.Buckner, C.L.Verlinde, E.Fan, W.G.Hol. Structures of Trypanosoma Brucei Methionyl-Trna Synthetase with Urea-Based Inhibitors Provide Guidance For Drug Design Against Sleeping Sickness. Plos Negl Trop Dis V. 8 E2775 2014.
ISSN: ISSN 1935-2727
PubMed: 24743796
DOI: 10.1371/JOURNAL.PNTD.0002775
Page generated: Sat Dec 12 01:44:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy