SMTL ID : 8k9v.1

Crystal structure of plasmodium LysRS complexing with ASP3026 derived LysRS inhibitor 3 (ADKI3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.209, A.231, E.233, R.255, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 Ligands: JT4.2 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:Y.430 Hydrogen bonds: A:G.209, A:N.428, A:E.432 Water bridges: A:R.255, A:R.255, A:R.255 Salt bridges: A:R.255 LYS.4: 13 residues within 4Å: Chain B: G.209, A.231, E.233, R.255, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 Ligands: JT4.5 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.430 Hydrogen bonds: B:G.209, B:E.233, B:E.271, B:E.271, B:Y.273, B:N.428, B:E.432, K.4 Water bridges: B:R.255, B:R.255, B:R.255 Salt bridges: B:R.255

2 x JT4: ~{N}4-(2,5-dimethoxyphenyl)-~{N}2-(2-propan-2-ylsulfonylphenyl)-1,3,5-triazine-2,4-diamine(Non-covalent)

JT4.2: 17 residues within 4Å: Chain A: N.211, 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.481, R.484, I.495 Ligands: LYS.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.255, A:E.257, A:F.267, A:F.267, A:E.425, A:N.428 Hydrogen bonds: A:R.255, A:N.264, A:N.264 Water bridges: A:G.481, A:D.483 pi-Stacking: A:H.263, A:F.267 JT4.5: 17 residues within 4Å: Chain B: 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, G.481, R.484, I.495 Ligands: LYS.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.255, B:E.257, B:F.267, B:F.267, B:E.425, B:N.428 Hydrogen bonds: B:R.255, B:N.264, B:N.264 pi-Stacking: B:H.263, B:F.267

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: I.183, R.187, I.250 Chain B: R.187, E.197, E.199, I.250 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.187, A:R.187, A:R.187 Water bridges: B:E.197, B:I.250

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

Related Entries With Identical Sequence