SMTL ID : 4qre.1

Structure of Methionyl-tRNA Synthetase in complex with 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 3BG: 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone(Non-covalent)

3BG.1: 21 residues within 4Å: Chain A: P.38, I.39, Y.41, D.78, H.80, G.81, T.160, Y.161, F.247, V.261, Y.262, V.263, W.264, D.266, A.267, N.270, Y.271, I.300, F.303, H.304 Ligands: ATP.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.80, A:F.247, A:Y.262, A:V.263, A:V.263, A:A.267, A:I.300, A:F.303 Hydrogen bonds: A:I.39, A:D.78, A:D.78, A:Y.161 Water bridges: A:D.78

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 21 residues within 4Å: Chain A: P.38, Y.40, H.47, G.49, H.50, Y.52, S.53, M.296, A.297, E.299, I.300, H.326, G.327, W.328, I.329, K.335, M.336, S.337, K.338 Ligands: 3BG.1, MG.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.53, A:A.297, A:E.299, A:I.329, A:I.329, A:M.336, A:S.337 Water bridges: A:S.43, A:K.335, A:K.335, A:K.338, A:K.338 Salt bridges: A:H.50, A:K.335, A:K.338, A:K.338 pi-Stacking: A:H.50

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.32, K.287 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:T.32, H2O.1, H2O.6, H2O.20, H2O.20, H2O.20 MG.4: 3 residues within 4Å: Chain A: K.335, S.337 Ligands: ATP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.337, H2O.22, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase. to be published

Release Date

2015-07-29

Peptides

Methionyl-tRNA synthetase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionyl-tRNA synthetase

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