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

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)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.112, L.113, K.116, L.251, R.255 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.352, A:R.352, A:R.370, A:R.370 GOL.3: 4 residues within 4Å: Chain A: H.58, K.107, W.228, A.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.107, A:A.229 GOL.4: 2 residues within 4Å: Chain A: R.177, A.180 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.177, A:R.177 Water bridges: A:R.184

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

DMS.5: 5 residues within 4Å: Chain A: F.88, E.89, Y.93, S.94, I.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.95

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 4 residues within 4Å: Chain A: R.40, V.44, S.483, P.487 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.487 Water bridges: A:R.40 Salt bridges: A:R.40

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

2EN.7: 18 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 15 PLIP interactions: 15 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:F.291, A:F.291 Hydrogen bonds: A:Y.19, A:D.56, A:D.56, 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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