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Arsenic in PDB 4mw6: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476), PDB code: 4mw6 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 / 2.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.277, 106.135, 207.057, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.1

Other elements in 4mw6:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) 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-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) (pdb code 4mw6). 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-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476), PDB code: 4mw6:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 4mw6

Go back to Arsenic Binding Sites List in 4mw6
Arsenic binding site 1 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)


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-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As318

b:44.1
occ:0.20
 AS A:CAS318 0.0 44.1 0.2
CE2 A:CAS318 2.0 44.2 0.2
CE1 A:CAS318 2.0 45.7 0.2
SG A:CAS318 2.2 43.6 1.0
CB A:CAS318 3.2 43.5 1.0
CG2 A:VAL566 3.5 69.2 1.0
CA A:CAS318 3.9 43.8 1.0
CG A:PRO565 4.0 70.7 1.0
C A:CAS318 4.6 42.5 1.0
O A:CAS318 4.6 41.3 1.0
CB A:VAL566 4.6 70.0 1.0
CG2 A:VAL260 4.7 38.5 1.0
CD A:PRO565 4.7 72.2 1.0
CG A:PRO255 4.8 41.6 1.0
O A:PRO255 4.8 42.6 1.0
N A:VAL566 4.9 67.2 1.0
OD1 A:ASP564 5.0 87.2 1.0

Arsenic binding site 2 out of 4 in 4mw6

Go back to Arsenic Binding Sites List in 4mw6
Arsenic binding site 2 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)


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-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As470

b:45.6
occ:0.70
 AS A:CAS470 0.0 45.6 0.7
CE2 A:CAS470 1.9 43.8 0.7
CE1 A:CAS470 2.0 46.0 0.7
SG A:CAS470 2.2 41.0 1.0
CB A:CAS470 3.2 38.2 1.0
CA A:CAS470 3.8 35.7 1.0
O A:HIS469 4.0 35.7 1.0
O A:ALA460 4.0 33.2 1.0
CB A:ARG453 4.1 42.8 1.0
CB A:ALA460 4.2 32.2 1.0
N A:CAS470 4.2 34.8 1.0
C A:ALA460 4.2 32.4 1.0
CA A:PRO462 4.3 33.7 1.0
C A:HIS469 4.4 35.0 1.0
N A:PRO462 4.4 33.3 1.0
C A:ILE461 4.5 32.1 1.0
O A:ILE461 4.6 32.3 1.0
CG A:PRO462 4.6 35.1 1.0
CA A:ALA460 4.6 32.9 1.0
CA A:ASN458 4.7 47.2 1.0
CA A:ARG453 4.7 41.5 1.0
N A:ALA460 4.7 35.2 1.0
N A:ILE461 4.8 31.6 1.0
CD A:PRO462 4.8 34.5 1.0
OD1 A:ASN458 4.8 51.2 1.0
CB A:PRO462 4.8 34.6 1.0
C A:ASN458 4.9 45.0 1.0

Arsenic binding site 3 out of 4 in 4mw6

Go back to Arsenic Binding Sites List in 4mw6
Arsenic binding site 3 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)


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-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As318

b:40.5
occ:0.20
 AS B:CAS318 0.0 40.5 0.2
CE1 B:CAS318 2.0 40.4 0.2
CE2 B:CAS318 2.0 41.5 0.2
SG B:CAS318 2.2 39.9 1.0
CB B:CAS318 3.2 39.6 1.0
CG2 B:VAL566 3.6 55.6 1.0
CA B:CAS318 3.9 40.4 1.0
OE1 B:GLN321 4.3 41.0 0.4
CB B:PRO255 4.5 44.6 1.0
O B:CAS318 4.6 37.3 1.0
C B:CAS318 4.6 38.9 1.0
CG2 B:VAL260 4.7 36.9 1.0
CB B:VAL566 4.8 55.5 1.0

Arsenic binding site 4 out of 4 in 4mw6

Go back to Arsenic Binding Sites List in 4mw6
Arsenic binding site 4 out of 4 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-(3-{[2-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476)


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-(Benzyloxy)-5-Chloro-3-(Prop-2-En-1-Yl)Benzyl]Amino}Propyl)- 3-Thiophen-3-Ylurea (Chem 1476) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As470

b:43.3
occ:0.70
 AS B:CAS470 0.0 43.3 0.7
CE2 B:CAS470 2.0 43.6 0.7
CE1 B:CAS470 2.0 43.1 0.7
SG B:CAS470 2.2 41.4 1.0
CB B:CAS470 3.1 39.6 1.0
CA B:CAS470 3.6 37.7 1.0
O B:ALA460 3.7 36.7 1.0
N B:PRO462 3.7 37.2 1.0
C B:ILE461 3.7 36.2 1.0
O B:ILE461 3.7 35.2 1.0
CA B:PRO462 3.8 37.0 1.0
C B:ALA460 3.9 37.3 1.0
O B:HIS469 4.1 36.2 1.0
N B:CAS470 4.2 37.1 1.0
CB B:ALA460 4.2 37.7 1.0
CG B:PRO462 4.2 37.9 1.0
CD B:PRO462 4.3 38.1 1.0
N B:ILE461 4.3 36.9 1.0
C B:HIS469 4.4 37.9 1.0
CB B:PRO462 4.4 37.5 1.0
CA B:ALA460 4.5 37.5 1.0
CA B:ILE461 4.5 36.5 1.0
CB B:ARG453 4.5 40.7 1.0
N B:ALA460 4.7 37.3 1.0
C B:CAS470 4.9 36.8 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 12:19:37 2024

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