SMTL ID : 9qdj.1

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD018870911

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 15 residues within 4Å: Chain A: G.232, A.233, A.254, 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 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.448 Hydrogen bonds: A:G.232, A:G.232, A:E.256, A:Y.296, A:E.450, K.1 Salt bridges: A:R.278 LYS.3: 15 residues within 4Å: Chain B: G.232, A.233, A.254, 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:E.450, K.3 Salt bridges: B:R.278

2 x 01: 2-azanyl-6-[(1~{S})-2,2-bis(fluoranyl)cyclohexyl]-4-methoxy-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one

01.2: 14 residues within 4Å: Chain A: R.278, T.285, H.286, S.287, F.290, M.292, E.443, T.446, G.497, M.498, G.499, R.502, I.512 Ligands: LYS.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.446 Hydrogen bonds: A:S.287, A:S.287 Water bridges: A:R.502 pi-Stacking: A:H.286, A:F.290 pi-Cation interactions: A:R.502 Halogen bonds: A:R.278 01.4: 14 residues within 4Å: Chain B: R.278, T.285, H.286, S.287, F.290, M.292, E.443, T.446, G.497, M.498, G.499, R.502, I.512 Ligands: LYS.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:T.446 Hydrogen bonds: B:S.287, B:S.287 Water bridges: B:R.502 pi-Stacking: B:H.286, B:F.290 pi-Cation interactions: B:R.502 Halogen bonds: B:R.278

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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