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Arsenic in PDB 4mw7: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469), PDB code: 4mw7 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 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.071, 105.862, 207.276, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.2

Other elements in 4mw7:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469) also contains other interesting chemical elements:

Iodine (I) 1 atom
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-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469) (pdb code 4mw7). 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-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469), PDB code: 4mw7:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4mw7

Go back to Arsenic Binding Sites List in 4mw7
Arsenic binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469)


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-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:50.1
occ:0.70
 AS A:CAS470 0.0 50.1 0.7
CE1 A:CAS470 2.0 50.5 0.7
CE2 A:CAS470 2.0 50.2 0.7
SG A:CAS470 2.2 44.1 1.0
CB A:CAS470 3.0 39.6 1.0
O A:ALA460 3.5 35.1 1.0
CA A:CAS470 3.5 37.2 1.0
CA A:PRO462 3.9 33.8 1.0
C A:ALA460 3.9 34.3 1.0
N A:PRO462 4.0 33.6 1.0
O A:HIS469 4.0 36.3 1.0
C A:ILE461 4.0 32.8 1.0
O A:ILE461 4.0 32.2 1.0
N A:CAS470 4.0 36.6 1.0
CB A:ALA460 4.2 34.0 1.0
C A:HIS469 4.3 35.9 1.0
CG A:PRO462 4.3 35.6 1.0
CB A:PRO462 4.4 35.0 1.0
CB A:ARG453 4.5 44.6 1.0
N A:ILE461 4.5 33.4 1.0
CA A:ALA460 4.5 34.6 1.0
CD A:PRO462 4.5 34.8 1.0
N A:ALA460 4.7 37.0 1.0
CA A:ILE461 4.8 32.9 1.0
CA A:ASN458 4.9 47.3 1.0
C A:CAS470 4.9 35.1 1.0
C A:ASN458 5.0 45.7 1.0

Arsenic binding site 2 out of 2 in 4mw7

Go back to Arsenic Binding Sites List in 4mw7
Arsenic binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(5-Chloro-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469)


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-2-Ethoxy-3-Iodobenzyl)Amino]Propyl}-3-Thiophen-3- Ylurea (Chem 1469) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:58.7
occ:0.70
 AS B:CAS470 0.0 58.7 0.7
CE2 B:CAS470 2.0 57.1 0.7
CE1 B:CAS470 2.0 57.1 0.7
SG B:CAS470 2.2 49.5 1.0
CB B:CAS470 3.1 45.4 1.0
CA B:CAS470 3.5 42.5 1.0
O B:ILE461 3.7 34.6 1.0
O B:ALA460 3.7 36.9 1.0
C B:ILE461 3.7 35.3 1.0
N B:PRO462 3.7 36.3 1.0
CA B:PRO462 3.8 36.5 1.0
C B:ALA460 3.9 36.0 1.0
O B:HIS469 4.0 39.1 1.0
N B:CAS470 4.1 41.6 1.0
CB B:ALA460 4.2 35.9 1.0
C B:HIS469 4.3 41.0 1.0
CB B:PRO462 4.3 37.5 1.0
N B:ILE461 4.3 35.9 1.0
CG B:PRO462 4.4 38.0 1.0
CA B:ALA460 4.5 36.0 1.0
CD B:PRO462 4.5 37.3 1.0
CA B:ILE461 4.6 35.9 1.0
N B:ALA460 4.6 37.4 1.0
O B:PRO467 4.8 47.0 1.0
C B:CAS470 4.9 40.0 1.0
CA B:ARG453 5.0 40.9 1.0
CG B:ARG453 5.0 45.1 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 12:19:50 2024

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