SMTL ID : 4zt3.1 (1 other biounit)

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1614)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x MET: METHIONINE(Non-covalent)

MET.1: 13 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, T.318, K.319 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: M.1, A:I.17, A:Y.19, A:D.56 Hydrophobic interactions: A:W.243, A:I.288 Salt bridges: A:K.319

1 x GOL: GLYCEROL(Non-functional Binders)

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

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

DMS.3: 5 residues within 4Å: Chain A: V.205, A.208, K.290, I.294 Ligands: DMS.4 No protein-ligand interaction detected (PLIP) DMS.4: 7 residues within 4Å: Chain A: E.161, K.286, D.287, I.288, L.289, K.290 Ligands: DMS.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.289, A:K.290 Salt bridges: A:E.161 DMS.5: 5 residues within 4Å: Chain A: F.139, T.141, P.214, K.290, Y.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.295 Water bridges: A:K.290 DMS.6: 5 residues within 4Å: Chain A: W.114, E.118, Y.174, V.232, P.233 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.118 DMS.7: 3 residues within 4Å: Chain A: R.40, S.483, P.487 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., 5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors. Acs Infect Dis. (2016)

Release Date

2016-05-04

Peptides

Methionyl-tRNA synthetase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionyl-tRNA synthetase

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