SMTL ID : 4mw6.1 (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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: V.109, E.112, L.113, K.116, L.251, R.255, L.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.109, A:E.112, A:R.255 GOL.2: 2 residues within 4Å: Chain A: R.352, R.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.352, A:R.352, A:R.370, A:R.370 GOL.3: 6 residues within 4Å: Chain A: R.40, V.44, S.483, P.487, S.490, V.491 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.40, A:S.483, A:P.487, A:S.490 GOL.4: 8 residues within 4Å: Chain A: Y.30, I.34, H.314, F.356, P.428, D.429, I.430, Q.431 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.30, A:D.429, A:D.429, A:I.430, A:Q.431 GOL.5: 3 residues within 4Å: Chain A: S.179, P.214, D.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.179, A:S.179, A:D.215 GOL.6: 1 residues within 4Å: Chain A: R.488 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.488, A:R.488

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

DMS.7: 5 residues within 4Å: Chain A: E.204, L.289, K.290 Ligands: DMS.8, DMS.9 No protein-ligand interaction detected (PLIP) DMS.8: 7 residues within 4Å: Chain A: E.161, K.286, D.287, I.288, L.289, K.290 Ligands: DMS.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.289 Salt bridges: A:E.161 DMS.9: 2 residues within 4Å: Chain A: L.213 Ligands: DMS.7 No protein-ligand interaction detected (PLIP)

1 x MET: METHIONINE(Non-covalent)

MET.10: 11 residues within 4Å: Chain A: P.16, I.17, Y.18, Y.19, D.56, W.243, A.246, L.247, Y.250, I.288, H.292 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.243 Hydrogen bonds: A:I.17, A:Y.19, A:D.56, M.10

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
A

Methionyl-tRNA synthetase

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