SMTL ID : 7wm7.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: 9I6.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.95, A:H.146, A:H.272 ZN.3: 4 residues within 4Å: Chain B: C.95, H.146, H.272 Ligands: 9I6.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.95, B:H.146, B:H.272

2 x 9I6: (2S,3R)-2-azanyl-N-[5-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)pentyl]-3-oxidanyl-N-[[3-(1-oxidanylidene-2,3-dihydroisoindol-5-yl)phenyl]methyl]butanamide(Non-covalent)

9I6.2: 21 residues within 4Å: Chain A: H.70, Y.74, A.77, M.78, P.92, M.93, C.95, R.124, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, T.243, H.272, A.274, S.278 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.243, A:H.272, A:A.274 Hydrogen bonds: A:V.137, A:Q.142 Water bridges: A:N.94, A:R.124 pi-Stacking: A:Y.74, A:Y.74, A:F.140, A:F.140 9I6.4: 22 residues within 4Å: Chain B: H.70, Y.74, A.77, M.78, P.92, M.93, C.95, R.124, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, T.243, H.272, R.273, A.274, S.278 Ligands: ZN.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.74, B:T.243, B:A.274 Hydrogen bonds: B:R.136, B:V.137, B:Q.142, B:D.144 pi-Stacking: B:Y.74, B:Y.74, B:F.140, B:F.140 pi-Cation interactions: B:R.136 Halogen bonds: B:A.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Z. et al., Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors against Aminoacyl-tRNA Synthetases. J.Med.Chem. (2022)

Release Date

2022-04-27

Peptides

Threonine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase

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