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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: Wed Jul 10 12:21:18 2024

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