SMTL ID : 6l2q.1

Threonyl-tRNA synthetase from Salmonella enterica in complex with an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.95, H.146, H.272 Ligands: E4O.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.95, A:H.146, A:H.272 ZN.4: 4 residues within 4Å: Chain B: C.95, H.146, H.272 Ligands: E4O.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.95, B:H.146, B:H.272

2 x E4O: (2S,3R)-2-azanyl-N-[(E)-4-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]but-2-enyl]-3-oxidanyl-butanamide(Non-covalent)

E4O.2: 16 residues within 4Å: Chain A: H.70, Y.74, A.77, M.78, P.92, M.93, C.95, R.124, Q.142, D.144, H.146, T.243, H.272, R.273, A.274 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.243, A:A.274 Hydrogen bonds: A:R.124, A:Q.142 Water bridges: A:C.95, A:Q.142, A:T.243 pi-Stacking: A:Y.74, A:Y.74 pi-Cation interactions: A:R.124 E4O.5: 16 residues within 4Å: Chain B: H.70, Y.74, A.77, M.78, P.92, M.93, C.95, R.124, Q.142, D.144, H.146, T.243, H.272, R.273, A.274 Ligands: ZN.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.92, B:T.243, B:H.272 Hydrogen bonds: B:R.124, B:Q.142 Water bridges: B:N.94 pi-Stacking: B:Y.74, B:Y.74

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

EDO.3: 2 residues within 4Å: Chain A: F.248, V.267 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.267, A:V.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, J. et al., Discovery of novel tRNA-amino acid dual-site inhibitors against threonyl-tRNA synthetase by fragment-based target hopping. Eur.J.Med.Chem. (2019)

Release Date

2020-01-15

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase

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