SMTL ID : 9qbr.1

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01991231

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, A.254, E.256, R.278, M.292, E.294, Y.296, Y.448, E.450, G.495, T.496, G.497 Ligands: 01.2 8 PLIP interactions: 1 Ligand-Ligand interactions, 7 interactions with chain A Hydrogen bonds: K.1, A:G.232, A:G.232, A:E.256, A:Y.296, A:E.450 Hydrophobic interactions: A:E.294 Salt bridges: A:R.278 LYS.3: 14 residues within 4Å: Chain B: G.232, A.233, A.254, E.256, R.278, M.292, E.294, Y.296, 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:E.294 Hydrogen bonds: B:G.232, B:G.232, B:E.450, K.3 Salt bridges: B:R.278

2 x 01: 2-azanyl-4-methoxy-6-(4-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, M.292, E.443, L.444, A.445, T.446, G.497, G.499, R.502, I.512 Ligands: LYS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.287, A:S.287, A:E.443, A:T.446 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, M.292, E.443, L.444, A.445, T.446, G.497, G.499, R.502, I.512 Ligands: LYS.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.287, B:S.287, B:E.443 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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