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TitleStructures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness.
Journal, issue, pagesPlos Negl Trop Dis, Vol. 8, Page e2775-e2775, Year 2014
Publish dateSep 24, 2013 (structure data deposition date)
AuthorsKoh, C.Y. / Kim, J.E. / Wetzel, A.B. / de van der Schueren, W.J. / Shibata, S. / Ranade, R.M. / Liu, J. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. ...Koh, C.Y. / Kim, J.E. / Wetzel, A.B. / de van der Schueren, W.J. / Shibata, S. / Ranade, R.M. / Liu, J. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G.
External linksPlos Negl Trop Dis / PubMed:24743796
MethodsX-ray diffraction
Resolution2.201 - 2.901 Å
Structure data

PDB-4mvw:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1433)
Method: X-RAY DIFFRACTION / Resolution: 2.901 Å

PDB-4mvx:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea (Chem 1356)
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-4mvy:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea (Chem 1387)
Method: X-RAY DIFFRACTION / Resolution: 2.314 Å

PDB-4mw0:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(2-hydroxyphenyl)urea (Chem 1392)
Method: X-RAY DIFFRACTION / Resolution: 2.201 Å

PDB-4mw1:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1444)
Method: X-RAY DIFFRACTION / Resolution: 2.494 Å

PDB-4mw2:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[5-chloro-2-hydroxy-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1472)
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-4mw4:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(5-chloro-2-hydroxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1473)
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-4mw5:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea (Chem 1415)
Method: X-RAY DIFFRACTION / Resolution: 2.347 Å

PDB-4mw6:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[2-(benzyloxy)-5-chloro-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1476)
Method: X-RAY DIFFRACTION / Resolution: 2.558 Å

PDB-4mw7:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(5-chloro-2-ethoxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1469)
Method: X-RAY DIFFRACTION / Resolution: 2.75 Å

PDB-4mw9:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-ethynylbenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1478)
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

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)
Method: X-RAY DIFFRACTION / Resolution: 2.313 Å

PDB-4mwc:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2-methyl-1-benzothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1540)
Method: X-RAY DIFFRACTION / Resolution: 2.649 Å

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
Method: X-RAY DIFFRACTION / Resolution: 2.253 Å

PDB-4mwe:
Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[5-chloro-3-(prop-2-en-1-yl)-2-(prop-2-en-1-yloxy)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1475)
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

Chemicals

ChemComp-GOL:
GLYCEROL

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-MET:
METHIONINE

ChemComp-SO4:
SULFATE ION

ChemComp-43E:
1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea

ChemComp-HOH:
WATER

ChemComp-C13:
1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea

ChemComp-387:
1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea

ChemComp-392:
1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(2-hydroxyphenyl)urea

ChemComp-44F:
1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-thiophen-3-ylurea

ChemComp-2E9:
1-(3-{[5-chloro-2-hydroxy-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea

ChemComp-2EB:
1-{3-[(5-chloro-2-hydroxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea

ChemComp-415:
1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea

ChemComp-2EE:
1-(3-{[2-(benzyloxy)-5-chloro-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea

ChemComp-2EF:
1-{3-[(5-chloro-2-ethoxy-3-iodobenzyl)amino]propyl}-3-thiophen-3-ylurea

ChemComp-2EJ:
1-{3-[(3-ethynylbenzyl)amino]propyl}-3-thiophen-3-ylurea

ChemComp-2EK:
1-(3-{[(2,5-dichlorothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea

ChemComp-2EM:
1-(3-{[(2-methyl-1-benzothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

ChemComp-2EN:
1-(3-{[5-chloro-3-(prop-2-en-1-yl)-2-(prop-2-en-1-yloxy)benzyl]amino}propyl)-3-thiophen-3-ylurea

Source
  • trypanosoma brucei (eukaryote)
KeywordsLIGASE/LIGASE INHIBITOR / aminoacyl-tRNA synthetase / aaRS / MetRS / parasite / protein-inhibitor complex / Rossmann fold / translation / nucleotide binding / LIGASE-LIGASE INHIBITOR complex

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