SMTL ID : 4zt5.2 (1 other biounit)

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine (Chem 1655)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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.2: 3 residues within 4Å: Chain A: E.8, R.48, E.275 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.8, A:E.8, A:R.48

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

DMS.3: 4 residues within 4Å: Chain A: F.88, E.89, Y.93, I.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.95 DMS.4: 3 residues within 4Å: Chain A: G.342, Y.343, D.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.343, A:D.344 Water bridges: A:A.345 Salt bridges: A:D.344

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

SO4.5: 4 residues within 4Å: Chain A: R.40, V.44, S.483, P.487 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.40, A:S.483 Salt bridges: A:R.40

1 x 4RN: (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine(Non-covalent)

4RN.6: 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.19, A:Y.19, A:H.58, A:A.246, A:L.247, A:I.288, A:I.288, A:F.291 Hydrogen bonds: A:D.56, A:D.56 Water bridges: A:H.58 Halogen bonds: A:Y.250

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
B

Methionyl-tRNA synthetase

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