SMTL ID : 8k9u.1

Crystal structure of plasmodium LysRS complexing with ASP3026 derived LysRS inhibitor 2 (ADKI2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 15 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.428, A.429, Y.430, E.432, G.477, L.478, G.479 Ligands: JSL.2 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:Y.430 Hydrogen bonds: A:Y.273, A:Y.273, A:N.428, A:E.432 Water bridges: A:R.255, A:R.255 Salt bridges: A:R.255 LYS.4: 11 residues within 4Å: Chain B: E.233, R.255, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 Ligands: JSL.5 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:E.271, B:Y.430 Hydrogen bonds: B:E.233, B:E.271, B:N.428, B:E.432, B:E.432, K.4 Salt bridges: B:R.255

2 x JSL: ~{N}4-(2,4-dimethoxyphenyl)-~{N}2-(2-propan-2-ylsulfonylphenyl)-1,3,5-triazine-2,4-diamine(Non-covalent)

JSL.2: 21 residues within 4Å: Chain A: N.211, A.212, R.255, E.257, G.258, T.262, H.263, N.264, P.265, F.267, E.418, E.425, V.426, L.427, N.428, G.479, L.480, G.481, R.484, I.495 Ligands: LYS.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.255, A:R.255, A:E.257, A:F.267, A:F.267, A:E.425 Hydrogen bonds: A:N.264, A:N.264, A:E.425, A:R.484 pi-Stacking: A:H.263, A:F.267 pi-Cation interactions: A:R.255 JSL.5: 19 residues within 4Å: Chain B: A.212, R.255, E.257, G.258, T.262, H.263, N.264, P.265, F.267, E.425, V.426, L.427, N.428, G.479, L.480, G.481, R.484, I.495 Ligands: LYS.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.255, B:R.255, B:E.257, B:F.267, B:F.267, B:E.425, B:N.428 Hydrogen bonds: B:N.264, B:N.264, B:R.484 pi-Stacking: B:H.263, B:F.267

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 10 residues within 4Å: Chain A: K.30, F.31, E.32, R.33 Chain B: W.274, A.275, Y.276, A.277, D.278, D.281 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.33, B:K.246, B:D.278, B:D.281

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Structure-guided conversion from an anaplastic lymphoma kinase inhibitor into Plasmodium lysyl-tRNA synthetase selective inhibitors. Commun Biol (2024)

Release Date

2024-06-26

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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