SMTL ID : 4mw1.2 (1 other biounit)

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1444)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: H.58, T.102, K.107, N.227, W.228, A.229, C.239 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.102, A:K.107, A:A.229, A:A.229 GOL.2: 3 residues within 4Å: Chain A: E.199, F.200, R.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.203, A:R.203 GOL.3: 5 residues within 4Å: Chain A: E.112, L.113, K.116, L.251, R.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.112, A:R.255 GOL.4: 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.5: 1 residues within 4Å: Chain A: R.488 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.488, A:R.488

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

DMS.6: 4 residues within 4Å: Chain A: E.89, Y.93, S.94, I.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.95 DMS.7: 2 residues within 4Å: Chain A: W.243 Ligands: 44F.8 No protein-ligand interaction detected (PLIP)

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

44F.8: 19 residues within 4Å: Chain A: P.16, I.17, Y.19, D.56, H.58, G.59, L.225, V.240, Y.241, V.242, W.243, D.245, A.246, L.247, Y.250, I.288, F.291, H.292 Ligands: DMS.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.19, A:H.58, A:A.246, A:I.288, A:I.288 Hydrogen bonds: A:Y.19, A:D.56, A:D.56 Water bridges: A:Y.19, A:D.56, A:D.56 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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