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Chlorine in PDB 4mvy: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387)

Enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387):
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-(3-Hydroxyphenyl)Urea (Chem 1387), PDB code: 4mvy 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 (°) 88.236, 105.995, 206.166, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.9

Other elements in 4mvy:

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor 1-{3-[(3,5-Dichlorobenzyl)Amino]Propyl}-3-(3-Hydroxyphenyl)Urea (Chem 1387) also contains other interesting chemical elements:

Arsenic (As) 2 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-(3-Hydroxyphenyl)Urea (Chem 1387) (pdb code 4mvy). 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-(3-Hydroxyphenyl)Urea (Chem 1387), PDB code: 4mvy:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4mvy

Go back to Chlorine Binding Sites List in 4mvy
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-(3-Hydroxyphenyl)Urea (Chem 1387)


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-(3-Hydroxyphenyl)Urea (Chem 1387) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl806

b:40.3
occ:1.00
 CLC B:387806 0.0 40.3 1.0
CAU B:387806 1.7 36.9 1.0
CAH B:387806 2.7 37.3 1.0
CAI B:387806 2.7 35.5 1.0
CE3 B:TRP474 3.4 20.7 1.0
CZ3 B:TRP474 3.6 21.9 1.0
CD2 B:PHE522 3.9 22.7 1.0
CAV B:387806 4.0 36.9 1.0
CG B:LEU478 4.0 21.9 1.0
CAW B:387806 4.0 36.2 1.0
CG2 B:VAL473 4.0 23.7 1.0
CB B:PHE522 4.1 22.1 1.0
CG B:PHE522 4.2 22.1 1.0
CD1 B:LEU478 4.2 22.6 1.0
CD2 B:LEU478 4.3 22.8 1.0
CB B:ALA477 4.4 22.3 1.0
CA B:TRP474 4.5 21.1 1.0
CAJ B:387806 4.5 35.0 1.0
O B:VAL473 4.5 22.1 1.0
CD2 B:TRP474 4.6 20.9 1.0
CG1 B:VAL473 4.6 23.8 1.0
CE2 B:PHE522 4.7 23.9 1.0
C B:VAL473 4.7 22.7 1.0
N B:TRP474 4.8 21.9 1.0
CH2 B:TRP474 4.9 22.6 1.0
CB B:VAL473 4.9 24.0 1.0

Chlorine binding site 2 out of 2 in 4mvy

Go back to Chlorine Binding Sites List in 4mvy
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-(3-Hydroxyphenyl)Urea (Chem 1387)


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-(3-Hydroxyphenyl)Urea (Chem 1387) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl806

b:41.7
occ:1.00
 CLD B:387806 0.0 41.7 1.0
CAV B:387806 1.8 36.9 1.0
CAH B:387806 2.7 37.3 1.0
CAJ B:387806 2.7 35.0 1.0
OH B:TYR481 3.4 21.0 1.0
N B:ILE248 3.5 21.5 1.0
NE2 B:HIS523 3.6 23.2 1.0
CE1 B:HIS523 3.7 23.6 1.0
CG1 B:ILE248 3.8 22.1 1.0
CA B:PRO247 3.9 21.9 1.0
CAU B:387806 4.0 36.9 1.0
CAW B:387806 4.0 36.2 1.0
CB B:PRO247 4.1 22.9 1.0
CZ B:TYR481 4.2 21.0 1.0
C B:PRO247 4.2 22.3 1.0
O B:ILE248 4.2 21.9 1.0
ND2 B:ASN480 4.3 21.5 1.0
CA B:ILE248 4.5 21.9 1.0
CAI B:387806 4.5 35.5 1.0
CE2 B:TYR481 4.6 20.0 1.0
O B:ALA477 4.6 22.7 1.0
CB B:ILE248 4.7 22.1 1.0
CD2 B:LEU478 4.7 22.8 1.0
CB B:ALA477 4.7 22.3 1.0
CD1 B:ILE248 4.8 22.2 1.0
CD1 B:ILE519 4.8 23.7 1.0
C B:ALA477 4.8 22.4 1.0
C B:ILE248 4.9 21.9 1.0
ND1 B:HIS523 5.0 23.4 1.0
CE1 B:TYR481 5.0 21.3 1.0
CD2 B:HIS523 5.0 22.9 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 19:19:29 2025

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