SMTL ID : 7cbg.1

Crystal structure of threonyl-tRNA synthetase (ThrRS) from Salmonella enterica in complex with an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

FQL.1: 15 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, H.272, R.273, A.274 Ligands: ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.74, A:R.124, A:A.274 Hydrogen bonds: A:H.70, A:R.124, A:Q.142 Water bridges: A:N.94, A:Y.223, A:T.243 pi-Stacking: A:Y.74, A:Y.74 pi-Cation interactions: A:R.124 FQL.3: 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.124, B:T.243, B:H.272, B:A.274 Hydrogen bonds: B:R.124, B:Q.142 Water bridges: B:N.94, B:Q.245 pi-Stacking: B:Y.74, B:Y.74 pi-Cation interactions: B:R.124

2 x ZN: ZINC ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, J. et al., Structure-guided optimization and mechanistic study of a class of quinazolinone-threonine hybrids as antibacterial ThrRS inhibitors. Eur.J.Med.Chem. (2020)

Release Date

2020-10-07

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase

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