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

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2,5-dichlorothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1509)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

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

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

DMS.4: 4 residues within 4Å: Chain A: E.89, Y.93, S.94, I.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.95 Water bridges: A:E.89 DMS.5: 1 residues within 4Å: Chain A: Y.241 No protein-ligand interaction detected (PLIP)

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

SO4.6: 5 residues within 4Å: Chain A: R.40, V.44, S.483, P.484, P.487 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.40, A:R.40, A:R.43, A:S.483 Salt bridges: A:R.40

1 x 2EK: 1-(3-{[(2,5-dichlorothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea(Non-covalent)

2EK.7: 17 residues within 4Å: Chain A: 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.19, A:H.58, A:I.288 Hydrogen bonds: A:Y.19, A:D.56, A:D.56 Water bridges: 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

Related Entries With Identical Sequence