Chlorine in PDB 5v49: Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917)

All present enzymatic activity of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917):
6.1.1.10;

The structure of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917), PDB code: 5v49 was solved by X.Barros-Alvarez, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	103.76 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	87.190, 106.200, 207.520, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 22.8

The binding sites of Chlorine atom in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917) (pdb code 5v49). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917), PDB code: 5v49:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917)


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 (Chem 1917) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:32.6 occ:1.00 CL2 B:8WA801 0.0 32.6 1.0 C16 B:8WA801 1.7 30.8 1.0 N4 B:8WA801 2.6 31.2 1.0 C15 B:8WA801 2.7 29.7 1.0 CD1 B:LEU456 3.6 37.9 1.0 CA B:GLY290 3.7 33.4 1.0 O B:VAL471 3.7 29.4 1.0 O B:HOH943 3.8 28.2 1.0 C17 B:8WA801 3.8 30.3 1.0 CD1 B:TYR472 3.8 30.3 1.0 C14 B:8WA801 4.0 30.0 1.0 N B:GLY290 4.0 32.6 1.0 CB B:ALA460 4.1 32.3 1.0 N B:VAL473 4.1 32.5 1.0 CA B:TYR472 4.1 29.9 1.0 CD2 B:LEU456 4.2 36.3 1.0 C B:TYR472 4.2 32.1 1.0 O B:HOH937 4.2 28.0 1.0 CE1 B:TYR472 4.4 29.5 1.0 C13 B:8WA801 4.4 30.2 1.0 CG B:LEU456 4.5 37.6 1.0 C B:HIS289 4.5 33.7 1.0 CB B:HIS289 4.6 32.9 1.0 C B:VAL471 4.7 30.4 1.0 CA B:VAL473 4.8 33.0 1.0 O B:TYR472 4.8 31.6 1.0 CG B:TYR472 4.9 29.2 1.0 O B:HIS289 4.9 34.6 1.0 O B:TRP459 4.9 32.6 1.0 N B:TYR472 4.9 30.0 1.0 C B:GLY290 4.9 33.3 1.0

Chlorine binding site 2 out of 3 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917)


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 (Chem 1917) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:36.9 occ:1.00 CL1 B:8WA801 0.0 36.9 1.0 C9 B:8WA801 1.7 35.2 1.0 C8 B:8WA801 2.7 35.4 1.0 C10 B:8WA801 2.7 33.6 1.0 CE3 B:TRP474 3.5 31.4 1.0 CZ3 B:TRP474 3.6 32.3 1.0 CD2 B:PHE522 3.8 30.7 1.0 CB B:PHE522 3.9 31.0 1.0 C7 B:8WA801 4.0 35.5 1.0 C11 B:8WA801 4.0 33.1 1.0 CG B:PHE522 4.0 28.9 1.0 CG2 B:VAL473 4.0 34.7 1.0 CG B:LEU478 4.2 30.6 1.0 CD1 B:LEU478 4.4 31.6 1.0 C6 B:8WA801 4.5 34.3 1.0 CD2 B:LEU478 4.5 32.2 1.0 O B:VAL473 4.6 31.5 1.0 CE2 B:PHE522 4.6 29.9 1.0 CG1 B:VAL473 4.7 35.7 1.0 CB B:ALA477 4.7 31.4 1.0 CA B:TRP474 4.7 30.2 1.0 CD2 B:TRP474 4.8 31.5 1.0 C B:VAL473 4.9 31.6 1.0 CH2 B:TRP474 4.9 32.5 1.0 CB B:VAL473 5.0 34.6 1.0 CD1 B:PHE522 5.0 28.8 1.0

Chlorine binding site 3 out of 3 in the Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Trypanosoma Brucei Methionyl-Trna Synthetase in Complex with Inhibitor (Chem 1917) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:41.8 occ:1.00 CL B:8WA801 0.0 41.8 1.0 C7 B:8WA801 1.7 35.5 1.0 C8 B:8WA801 2.7 35.4 1.0 C6 B:8WA801 2.7 34.3 1.0 N2 B:8WA801 3.0 34.4 1.0 OH B:TYR481 3.6 28.7 1.0 N B:ILE248 3.6 28.2 1.0 CE1 B:HIS523 3.7 30.6 1.0 NE2 B:HIS523 3.8 30.6 1.0 CA B:PRO247 3.9 29.1 1.0 CB B:PRO247 3.9 29.6 1.0 CG1 B:ILE248 4.0 30.5 1.0 C9 B:8WA801 4.0 35.2 1.0 C11 B:8WA801 4.0 33.1 1.0 O B:ILE248 4.1 28.4 1.0 C B:PRO247 4.2 29.5 1.0 CD1 B:ILE519 4.4 33.1 1.0 C5 B:8WA801 4.4 33.6 1.0 CZ B:TYR481 4.4 28.5 1.0 C10 B:8WA801 4.5 33.6 1.0 CA B:ILE248 4.6 29.0 1.0 ND2 B:ASN480 4.8 27.9 1.0 C B:ILE248 4.8 29.1 1.0 CB B:ALA477 4.8 31.4 1.0 CB B:ILE248 4.9 29.2 1.0 CE2 B:TYR481 4.9 30.0 1.0 O B:ALA477 5.0 30.9 1.0

W.Huang, Z.Zhang, R.M.Ranade, J.R.Gillespie, X.Barros-Alvarez, S.A.Creason, S.Shibata, C.L.M.J.Verlinde, W.G.J.Hol, F.S.Buckner, E.Fan. Optimization of A Binding Fragment Targeting the "Enlarged Methionine Pocket" Leads to Potent Trypanosoma Brucei Methionyl-Trna Synthetase Inhibitors. Bioorg. Med. Chem. Lett. V. 27 2702 2017.
ISSN: ESSN 1464-3405
PubMed: 28465105
DOI: 10.1016/J.BMCL.2017.04.048