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Chlorine 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:

Arsenic (As) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4mwb

Go back to Chlorine Binding Sites List in 4mwb
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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
B:Cl807

b:63.9
occ:1.00
 CL1 B:2EK807 0.0 63.9 1.0
C3 B:2EK807 1.7 49.3 1.0
C2 B:2EK807 2.7 45.7 1.0
S B:2EK807 2.9 49.7 1.0
C4 B:2EK807 3.2 41.0 1.0
CD2 B:PHE522 3.5 25.7 1.0
CZ3 B:TRP474 3.6 23.8 1.0
C5 B:2EK807 3.6 33.6 1.0
N B:2EK807 3.9 36.6 1.0
C1 B:2EK807 3.9 47.1 1.0
CE2 B:PHE522 3.9 26.1 1.0
CG2 B:VAL473 4.0 24.8 1.0
C B:2EK807 4.1 50.2 1.0
CE3 B:TRP474 4.1 23.1 1.0
CG B:PHE522 4.3 25.3 1.0
O B:DMS805 4.4 74.8 1.0
CH2 B:TRP474 4.5 24.7 1.0
CG1 B:VAL473 4.5 24.8 1.0
O B:HOH1113 4.5 34.1 1.0
CB B:PHE522 4.7 25.2 1.0
CB B:VAL473 4.9 24.8 1.0
CG2 B:ILE519 5.0 28.6 1.0
CZ B:PHE522 5.0 26.0 1.0

Chlorine binding site 2 out of 2 in 4mwb

Go back to Chlorine Binding Sites List in 4mwb
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
B:Cl807

b:51.8
occ:1.00
 CL B:2EK807 0.0 51.8 1.0
C B:2EK807 1.7 50.2 1.0
C1 B:2EK807 2.7 47.1 1.0
S B:2EK807 3.0 49.7 1.0
OH B:TYR481 3.5 22.6 1.0
NE2 B:HIS523 3.6 23.4 1.0
CE1 B:HIS523 3.7 23.7 1.0
N B:ILE248 3.8 23.7 1.0
CG1 B:ILE248 3.8 24.0 1.0
C2 B:2EK807 4.0 45.7 1.0
C3 B:2EK807 4.1 49.3 1.0
CD2 B:LEU478 4.1 24.2 1.0
ND2 B:ASN480 4.1 23.8 1.0
CZ B:TYR481 4.1 23.1 1.0
O B:ALA477 4.2 25.0 1.0
CA B:PRO247 4.3 23.6 1.0
CE2 B:TYR481 4.4 22.9 1.0
O B:ILE248 4.5 23.2 1.0
C B:ALA477 4.5 24.1 1.0
CB B:ALA477 4.5 24.1 1.0
CB B:PRO247 4.5 24.1 1.0
C B:PRO247 4.6 23.8 1.0
CA B:ILE248 4.7 23.5 1.0
CA B:LEU478 4.8 23.7 1.0
N B:LEU478 4.8 23.8 1.0
CD1 B:ILE248 4.8 24.2 1.0
CB B:ILE248 4.8 23.8 1.0
CD2 B:HIS523 4.9 23.2 1.0
CG B:LEU478 5.0 23.8 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: Fri Jul 11 19:20:39 2025

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