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Chlorine in PDB 4mvw: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433):
6.1.1.10;

Protein crystallography data

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433), PDB code: 4mvw 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 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.066, 105.858, 206.974, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.9

Other elements in 4mvw:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) 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-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) (pdb code 4mvw). 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-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433), PDB code: 4mvw:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4mvw

Go back to Chlorine Binding Sites List in 4mvw
Chlorine binding site 1 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)


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-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl807

b:47.0
occ:1.00
 CLB B:43E807 0.0 47.0 1.0
CAS B:43E807 1.7 43.6 1.0
CAH B:43E807 2.7 42.2 1.0
CAG B:43E807 2.7 44.5 1.0
CE3 B:TRP474 3.3 25.7 1.0
CZ3 B:TRP474 3.5 26.3 1.0
CD2 B:PHE522 3.9 28.8 1.0
CG B:LEU478 3.9 27.1 1.0
CAT B:43E807 4.0 45.1 1.0
CAU B:43E807 4.0 41.9 1.0
CB B:PHE522 4.0 27.5 1.0
CG2 B:VAL473 4.0 28.5 1.0
CD2 B:LEU478 4.1 28.0 1.0
CG B:PHE522 4.2 28.1 1.0
CD1 B:LEU478 4.4 27.0 1.0
O B:VAL473 4.4 26.6 1.0
CG1 B:VAL473 4.5 27.8 1.0
CA B:TRP474 4.5 26.1 1.0
CAI B:43E807 4.5 43.8 1.0
CB B:ALA477 4.5 28.9 1.0
CD2 B:TRP474 4.6 25.9 1.0
CE2 B:PHE522 4.7 30.3 1.0
C B:VAL473 4.7 27.2 1.0
CB B:VAL473 4.8 28.4 1.0
CH2 B:TRP474 4.8 27.3 1.0
N B:TRP474 4.8 26.8 1.0
N B:LEU478 4.9 27.1 1.0
O B:TRP474 5.0 26.8 1.0

Chlorine binding site 2 out of 2 in 4mvw

Go back to Chlorine Binding Sites List in 4mvw
Chlorine binding site 2 out of 2 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433)


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-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-Thiophen-3-Ylurea (Chem 1433) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl807

b:46.6
occ:1.00
 CLC B:43E807 0.0 46.6 1.0
CAT B:43E807 1.7 45.1 1.0
CAG B:43E807 2.7 44.5 1.0
CAI B:43E807 2.7 43.8 1.0
OH B:TYR481 3.5 25.2 1.0
NE2 B:HIS523 3.6 30.4 1.0
CE1 B:HIS523 3.6 30.2 1.0
N B:ILE248 3.7 27.2 1.0
CB B:PRO247 3.9 28.4 1.0
CG1 B:ILE248 3.9 26.7 1.0
CAS B:43E807 4.0 43.6 1.0
CA B:PRO247 4.0 27.9 1.0
CAU B:43E807 4.0 41.9 1.0
CZ B:TYR481 4.2 25.3 1.0
ND2 B:ASN480 4.2 28.0 1.0
O B:ILE248 4.3 27.1 1.0
C B:PRO247 4.4 27.7 1.0
CAH B:43E807 4.5 42.2 1.0
CE2 B:TYR481 4.5 25.1 1.0
CA B:ILE248 4.7 26.8 1.0
CB B:ALA477 4.7 28.9 1.0
CD2 B:LEU478 4.7 28.0 1.0
O B:ALA477 4.8 27.9 1.0
CD1 B:ILE519 4.8 29.6 1.0
C B:ALA477 4.8 27.7 1.0
CD1 B:ILE248 4.9 26.8 1.0
CB B:ILE248 4.9 26.6 1.0
ND1 B:HIS523 4.9 29.9 1.0
N B:LEU478 4.9 27.1 1.0
C B:ILE248 4.9 27.3 1.0
CD2 B:HIS523 5.0 29.3 1.0
CA B:LEU478 5.0 27.1 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: Fri Jul 11 19:18:58 2025

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