SMTL ID : 9qei.1

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01866774

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 14 residues within 4Å: Chain A: G.232, A.233, E.256, R.278, M.292, E.294, Y.296, T.446, Y.448, E.450, G.495, T.496, G.497 Ligands: 01.2 7 PLIP interactions: 1 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: K.1, A:G.232, A:G.232, A:Y.296, A:Y.296 Hydrophobic interactions: A:Y.448 Salt bridges: A:R.278 LYS.3: 14 residues within 4Å: Chain B: G.232, A.233, E.256, R.278, M.292, E.294, Y.296, T.446, Y.448, E.450, G.495, T.496, G.497 Ligands: 01.4 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.448 Hydrogen bonds: B:G.232, B:G.232, B:Y.296, K.3 Salt bridges: B:R.278

2 x 01: 2-azanyl-4-ethoxy-6-[(1~{R},2~{S})-2-oxidanylcyclohexyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one

01.2: 15 residues within 4Å: Chain A: R.278, T.285, H.286, S.287, F.290, E.443, L.444, A.445, T.446, G.497, G.499, D.501, R.502, I.512 Ligands: LYS.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.446, A:D.501, A:I.512 Hydrogen bonds: A:S.287, A:S.287, A:R.502 pi-Stacking: A:F.290 pi-Cation interactions: A:H.286 01.4: 15 residues within 4Å: Chain B: R.278, T.285, H.286, S.287, F.290, E.443, L.444, A.445, T.446, G.497, G.499, D.501, R.502, I.512 Ligands: LYS.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.446, B:D.501, B:I.512 Hydrogen bonds: B:S.287, B:S.287, B:R.502 pi-Stacking: B:F.290 pi-Cation interactions: B:H.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davis, S.H. et al., Design and Development of Lysyl tRNA Synthetase Inhibitors, for the Treatment of Tuberculosis. J.Med.Chem. (2025)

Release Date

2025-08-13

Peptides

Lysine--tRNA ligase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Lysine--tRNA ligase 1

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