SMTL ID : 7wpi.1

Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x 1V7: 2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide(Non-covalent)

1V7.1: 19 residues within 4Å: Chain A: P.21, I.22, Y.24, D.61, H.63, G.64, E.142, V.244, Y.245, V.246, W.247, A.250, L.251, Y.254, I.283, F.286, H.287 Ligands: EDO.3, EDO.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.21, A:I.22, A:Y.245, A:V.246, A:W.247, A:A.250, A:L.251, A:I.283, A:F.286, A:F.286 Hydrogen bonds: A:D.61, A:H.63 Water bridges: A:D.61, A:E.62, A:K.66 pi-Stacking: A:Y.24, A:Y.24 Halogen bonds: A:V.244

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: H.63, T.107, K.112, W.232, G.233 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.232 Salt bridges: A:H.63, A:K.112

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: Y.144, Y.245 Ligands: 1V7.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.245 Water bridges: A:Q.65 EDO.4: 5 residues within 4Å: Chain A: P.21, I.22, Y.23, I.283 Ligands: 1V7.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, J. et al., Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Nucleic Acids Res. (2022)

Release Date

2022-04-27

Peptides

Methionine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine--tRNA ligase

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