SMTL ID : 4mw0.2 (1 other biounit)

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(2-hydroxyphenyl)urea (Chem 1392)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.112, K.116, L.251, R.255, L.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.112, A:E.112, A:R.255 GOL.2: 2 residues within 4Å: Chain A: R.352, R.370 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.352, A:R.352, A:R.370, A:R.370 Water bridges: A:E.353 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:R.40, A:P.487, A:S.490 GOL.4: 7 residues within 4Å: Chain A: H.58, T.102, K.107, N.227, W.228, A.229, C.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.107, A:N.227, A:A.229 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 GOL.6: 2 residues within 4Å: Chain A: M.5, E.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.8

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

DMS.7: 3 residues within 4Å: Chain A: Y.241, W.243, F.291 No protein-ligand interaction detected (PLIP)

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

392.8: 18 residues within 4Å: Chain A: P.16, I.17, Y.19, D.56, H.58, G.59, E.137, L.225, V.240, Y.241, V.242, W.243, D.245, A.246, L.247, Y.250, I.288, H.292 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.19, A:H.58, A:L.225, A:Y.241, A:V.242, A:A.246, A:L.247 Hydrogen bonds: A:Y.19, A:Y.19, A:D.56, A:D.56 Water bridges: A:D.56, A:D.56, A:Q.60 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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