SMTL ID : 4mw6.2 (1 other biounit)

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)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: E.112, L.113, K.116, L.251, R.255, F.271, L.305 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.112, A:E.112, A:R.255 Water bridges: A:R.255 GOL.2: 2 residues within 4Å: Chain A: R.352, R.370 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.352, A:R.370, A:R.370 GOL.3: 4 residues within 4Å: Chain A: R.40, R.43, V.44, S.483 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:R.40, A:R.43, A:R.43 GOL.4: 3 residues within 4Å: Chain A: S.325, K.326, S.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.326, A:S.327, A:S.327

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 4 residues within 4Å: Chain A: F.88, E.89, Y.93, I.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.95

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

2EE.6: 15 residues within 4Å: Chain A: P.16, I.17, Y.19, D.56, H.58, G.59, Y.241, V.242, W.243, D.245, A.246, L.247, Y.250, F.291, H.292 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:H.58, A:V.242, A:V.242, A:W.243, A:W.243, A:A.246, A:L.247, A:L.247, A:F.291 Hydrogen bonds: A:Y.19, A:D.56, A:D.56, A:D.56, A:D.56 pi-Stacking: A:F.291 Halogen bonds: A:Y.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koh, C.Y. et al., Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness. Plos Negl Trop Dis (2014)

Release Date

2014-04-30

Peptides

Methionyl-tRNA synthetase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Methionyl-tRNA synthetase

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