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

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) and Atp Analog Amppcp

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) and Atp Analog Amppcp:
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) and Atp Analog Amppcp, PDB code: 4mwd 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 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.267, 105.880, 206.676, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.1

Other elements in 4mwd:

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) and Atp Analog Amppcp 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) and Atp Analog Amppcp (pdb code 4mwd). 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) and Atp Analog Amppcp, PDB code: 4mwd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4mwd

Go back to Chlorine Binding Sites List in 4mwd
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) and Atp Analog Amppcp


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) and Atp Analog Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl808

b:38.9
occ:1.00
 CLB B:43E808 0.0 38.9 1.0
CAS B:43E808 1.8 34.1 1.0
CAG B:43E808 2.7 34.3 1.0
CAH B:43E808 2.7 32.8 1.0
OH B:TYR481 3.5 25.7 1.0
N B:ILE248 3.5 25.3 1.0
NE2 B:HIS523 3.6 27.4 1.0
CE1 B:HIS523 3.7 27.3 1.0
CG1 B:ILE248 3.8 25.4 1.0
CA B:PRO247 3.9 25.0 1.0
CAT B:43E808 4.0 33.2 1.0
CAU B:43E808 4.0 32.2 1.0
CB B:PRO247 4.0 25.7 1.0
CZ B:TYR481 4.2 25.0 1.0
C B:PRO247 4.2 25.1 1.0
O B:ILE248 4.3 25.1 1.0
ND2 B:ASN480 4.4 24.1 1.0
O B:ALA477 4.5 25.5 1.0
CAI B:43E808 4.5 32.4 1.0
CA B:ILE248 4.6 25.4 1.0
CD2 B:LEU478 4.6 26.1 1.0
CE2 B:TYR481 4.7 24.9 1.0
CB B:ALA477 4.7 25.4 1.0
CB B:ILE248 4.7 25.3 1.0
C B:ALA477 4.8 24.9 1.0
CD1 B:ILE248 4.8 25.6 1.0
CD1 B:ILE519 4.9 27.6 1.0
C B:ILE248 4.9 25.6 1.0
ND1 B:HIS523 4.9 26.8 1.0
CD2 B:HIS523 5.0 25.9 1.0

Chlorine binding site 2 out of 2 in 4mwd

Go back to Chlorine Binding Sites List in 4mwd
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) and Atp Analog Amppcp


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) and Atp Analog Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl808

b:38.4
occ:1.00
 CLC B:43E808 0.0 38.4 1.0
CAT B:43E808 1.7 33.2 1.0
CAI B:43E808 2.7 32.4 1.0
CAG B:43E808 2.7 34.3 1.0
CE3 B:TRP474 3.4 25.1 1.0
CZ3 B:TRP474 3.5 25.8 1.0
CD2 B:PHE522 4.0 28.3 1.0
CAS B:43E808 4.0 34.1 1.0
CAU B:43E808 4.0 32.2 1.0
CG B:LEU478 4.0 25.6 1.0
CB B:PHE522 4.1 26.8 1.0
CG2 B:VAL473 4.2 25.3 1.0
CG B:PHE522 4.2 27.4 1.0
CD2 B:LEU478 4.2 26.1 1.0
CD1 B:LEU478 4.3 26.0 1.0
CAH B:43E808 4.5 32.8 1.0
CG1 B:VAL473 4.5 25.8 1.0
CB B:ALA477 4.5 25.4 1.0
CA B:TRP474 4.6 23.8 1.0
CD2 B:TRP474 4.6 25.1 1.0
O B:VAL473 4.6 23.6 1.0
CE2 B:PHE522 4.7 29.7 1.0
C B:VAL473 4.8 24.1 1.0
CH2 B:TRP474 4.8 26.2 1.0
N B:TRP474 4.9 24.2 1.0
CB B:VAL473 4.9 25.5 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 19:20:46 2025

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