SMTL ID : 4hwp.1

Crystal structure of E. coli Threonyl-tRNA synthetase bound to a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: X16.2 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: X16.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.95, B:H.146, B:H.272

2 x X16: N-{[3-(4-amino-2-methylquinazolin-7-yl)phenyl]sulfonyl}-L-threoninamide(Non-covalent)

X16.2: 23 residues within 4Å: Chain A: M.93, C.95, R.124, E.126, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, K.226, Q.240, T.243, Q.245, H.272, R.273, A.274, G.277, S.278, R.281 Ligands: ZN.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.124, A:E.126, A:A.274 Hydrogen bonds: A:R.124, A:R.124, A:M.135, A:V.137, A:Q.142, A:Y.223, A:Q.240, A:Q.245, A:Q.245, A:R.281 Water bridges: A:N.94, A:D.144, A:S.278 pi-Stacking: A:F.140, A:F.140 X16.4: 23 residues within 4Å: Chain B: M.93, C.95, R.124, E.126, M.135, R.136, V.137, F.140, Q.142, D.144, H.146, Y.223, K.226, Q.240, T.243, Q.245, H.272, R.273, A.274, G.277, S.278, R.281 Ligands: ZN.3 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.124, B:E.126, B:T.243 Hydrogen bonds: B:R.124, B:R.124, B:M.135, B:V.137, B:Q.142, B:Y.223, B:K.226, B:Q.240, B:Q.245, B:Q.245, B:R.281 Water bridges: B:Y.74, B:N.94, B:D.144, B:S.278 pi-Stacking: B:F.140, B:F.140

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Threonine--tRNA ligase

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