SMTL ID : 4hwt.1

Crystal structure of human Threonyl-tRNA synthetase bound to a novel 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: 1B2.2 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: 1B2.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.95, B:H.146, B:H.272

2 x 1B2: N-{[3-(2H-INDAZOL-5-YL)PHENYL]SULFONYL}-L-THREONINAMIDE(Non-covalent)

1B2.2: 18 residues within 4Å: Chain A: M.93, C.95, R.124, Q.142, D.144, H.146, Y.222, K.225, D.227, I.228, Q.239, C.240, A.241, T.242, Q.244, H.272, R.273 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.227, A:Q.239, A:T.242, A:H.272 Hydrogen bonds: A:R.124, A:R.124, A:Q.142, A:Y.222, A:I.228, A:Q.244, A:Q.244 Water bridges: A:C.95, A:C.95 1B2.4: 20 residues within 4Å: Chain B: M.93, C.95, R.124, Q.142, D.144, H.146, Y.222, K.225, D.227, I.228, Q.229, Q.239, C.240, A.241, T.242, Q.244, H.272, R.273, A.274 Ligands: ZN.3 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.227, B:Q.239, B:T.242, B:A.274 Hydrogen bonds: B:R.124, B:R.124, B:Q.142, B:D.144, B:Y.222, B:K.225, B:Q.244, B:Q.244, B:R.273 Water bridges: B:N.94, B:D.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Teng, M. et al., Identification of bacteria-selective threonyl-tRNA synthetase substrate inhibitors by structure-based design. J.Med.Chem. (2013)

Release Date

2013-09-18

Peptides

Threonine--tRNA ligase, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase, cytoplasmic