Atomistry » Arsenic » PDB 4j9t-4mwc » 4mw6
Atomistry »
  Arsenic »
    PDB 4j9t-4mwc »
      4mw6 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy