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Arsenic in PDB 4mwb: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509), PDB code: 4mwb 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 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.138, 106.171, 206.975, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 19.8

Other elements in 4mwb:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509) (pdb code 4mwb). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509), PDB code: 4mwb:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4mwb

Go back to Arsenic Binding Sites List in 4mwb
Arsenic binding site 1 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509)


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-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:42.6
occ:0.50
 AS A:CAS318 0.0 42.6 0.5
CE1 A:CAS318 2.0 41.7 0.5
CE2 A:CAS318 2.0 43.8 0.5
SG A:CAS318 2.2 39.6 1.0
CB A:CAS318 3.1 38.0 1.0
CG2 A:VAL566 3.8 63.1 1.0
CA A:CAS318 3.9 37.0 1.0
CG2 A:VAL260 4.5 28.9 1.0
C A:CAS318 4.6 35.5 1.0
O A:CAS318 4.7 33.5 1.0
CG A:PRO255 4.7 36.0 1.0
O A:HOH979 4.7 48.5 1.0
O A:PRO255 4.8 36.1 1.0
CD A:PRO565 4.9 62.8 1.0
OD1 A:ASP564 4.9 73.3 1.0
CG A:PRO565 4.9 60.6 1.0
CB A:PRO255 4.9 35.1 1.0

Arsenic binding site 2 out of 4 in 4mwb

Go back to Arsenic Binding Sites List in 4mwb
Arsenic binding site 2 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509)


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-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:32.3
occ:0.70
 AS A:CAS470 0.0 32.3 0.7
CE2 A:CAS470 2.0 33.5 0.7
CE1 A:CAS470 2.0 33.2 0.7
SG A:CAS470 2.2 32.2 1.0
CB A:CAS470 3.1 29.6 1.0
CA A:CAS470 3.5 28.3 1.0
O A:ALA460 3.7 29.2 1.0
N A:PRO462 3.8 28.8 1.0
CA A:PRO462 3.8 29.1 1.0
C A:ILE461 3.8 27.6 1.0
O A:ILE461 3.9 27.0 1.0
C A:ALA460 3.9 28.9 1.0
O A:HIS469 4.1 28.5 1.0
N A:CAS470 4.2 28.2 1.0
CG A:PRO462 4.2 30.6 1.0
CB A:ALA460 4.2 28.7 1.0
CD A:PRO462 4.3 29.8 1.0
N A:ILE461 4.3 27.8 1.0
CB A:PRO462 4.4 30.1 1.0
C A:HIS469 4.4 28.0 1.0
CA A:ALA460 4.5 29.1 1.0
CB A:ARG453 4.6 31.3 1.0
CA A:ILE461 4.6 27.8 1.0
N A:ALA460 4.7 30.6 1.0
C A:CAS470 4.9 27.4 1.0

Arsenic binding site 3 out of 4 in 4mwb

Go back to Arsenic Binding Sites List in 4mwb
Arsenic binding site 3 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:37.1
occ:0.50
 AS B:CAS318 0.0 37.1 0.5
CE2 B:CAS318 2.0 38.3 0.5
CE1 B:CAS318 2.0 39.6 0.5
SG B:CAS318 2.2 36.7 1.0
CB B:CAS318 3.1 36.7 1.0
CA B:CAS318 3.9 36.5 1.0
CB B:PRO255 4.0 36.3 1.0
O B:HOH1038 4.2 46.6 1.0
CG2 B:VAL260 4.4 28.5 1.0
CG2 B:VAL566 4.5 47.4 1.0
O B:HOH968 4.5 39.7 1.0
O B:HOH1110 4.6 43.6 1.0
C B:CAS318 4.7 34.6 1.0
O B:PRO255 4.7 37.2 1.0
O B:CAS318 4.7 34.2 1.0
CG B:PRO255 4.8 36.5 1.0
C B:PRO255 4.9 36.4 1.0

Arsenic binding site 4 out of 4 in 4mwb

Go back to Arsenic Binding Sites List in 4mwb
Arsenic binding site 4 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[(2,5-Dichlorothiophen-3-Yl)Methyl]Amino}Propyl)-3-Thiophen-3- Ylurea (Chem 1509) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:29.0
occ:0.70
 AS B:CAS470 0.0 29.0 0.7
CE2 B:CAS470 2.0 30.1 0.7
CE1 B:CAS470 2.0 29.8 0.7
SG B:CAS470 2.2 29.4 1.0
CB B:CAS470 3.1 27.7 1.0
O B:ALA460 3.5 29.4 1.0
CA B:CAS470 3.7 26.8 1.0
N B:PRO462 3.7 28.5 1.0
CA B:PRO462 3.7 28.4 1.0
O B:ILE461 3.7 27.9 1.0
C B:ILE461 3.8 28.0 1.0
C B:ALA460 3.8 28.4 1.0
O B:HIS469 4.1 26.9 1.0
CB B:ALA460 4.1 27.2 1.0
N B:CAS470 4.3 26.6 1.0
CD B:PRO462 4.3 29.0 1.0
CB B:PRO462 4.3 29.2 1.0
CG B:PRO462 4.4 29.5 1.0
N B:ILE461 4.4 27.7 1.0
C B:HIS469 4.4 27.5 1.0
O B:HOH1033 4.4 38.7 1.0
CA B:ALA460 4.4 27.7 1.0
N B:ALA460 4.6 28.1 1.0
CA B:ILE461 4.6 28.1 1.0
CB B:ARG453 4.6 27.6 1.0
C B:CAS470 5.0 26.1 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: Sun Jul 6 23:52:55 2025

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