SMTL ID : 7wmf.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 9I9: (2S,3R)-2-azanyl-N-[(1R)-2-[3-[6,7-bis(chloranyl)-4-oxidanylidene-quinazolin-3-yl]propanoylamino]-1-[3-[4-(trifluoromethyl)phenyl]phenyl]ethyl]-3-oxidanyl-butanamide(Non-covalent)

9I9.1: 23 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, R.273, A.274, G.277, S.278 Ligands: ZN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.140, A:F.140, A:T.243, A:H.272, A:A.274 Hydrogen bonds: A:R.124, A:Q.142 Water bridges: A:N.94, A:Q.142, A:Y.223, A:Y.223, A:T.243 pi-Stacking: A:Y.74, A:Y.74 Halogen bonds: A:A.77, A:M.135 9I9.4: 23 residues within 4Å: Chain B: H.70, Y.74, A.77, M.78, P.92, M.93, C.95, R.124, E.126, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, T.243, H.272, R.273, A.274, G.277 Ligands: ZN.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.74, B:H.272, B:A.274 Hydrogen bonds: B:R.124, B:R.124, B:Q.142, B:R.273 pi-Stacking: B:Y.74, B:Y.74, B:F.140 pi-Cation interactions: B:R.124 Halogen bonds: B:E.126, B:M.135

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

EDO.2: 7 residues within 4Å: Chain A: T.68, H.70, Y.223, D.247, S.249, L.250, R.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.68, A:H.272

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.95, H.146, H.272 Ligands: 9I9.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.95, A:H.146, A:H.272 ZN.5: 4 residues within 4Å: Chain B: C.95, H.146, H.272 Ligands: 9I9.4 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

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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