SMTL ID : 8k9w.1

Crystal structure of plasmodium LysRS complexing with ASP3026 derived LysRS inhibitor 4 (ADKI4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

JTR.1: 15 residues within 4Å: Chain A: R.255, E.257, G.258, T.262, H.263, N.264, P.265, F.267, E.425, V.426, L.427, G.479, G.481, R.484, I.495 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.255, A:R.255, A:E.257, A:F.267, A:E.425 Hydrogen bonds: A:N.264, A:N.264 pi-Stacking: A:H.263, A:F.267 pi-Cation interactions: A:R.484 JTR.4: 16 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, G.479, L.480, G.481, R.484, I.495 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.255, B:E.257, B:F.267, B:F.267 Hydrogen bonds: B:N.264, B:N.264 Water bridges: B:R.484 pi-Stacking: B:H.263, B:F.267

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

MES.2: 8 residues within 4Å: Chain A: W.274, A.275, Y.276, D.278, D.281 Chain B: F.31, E.32, R.33 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.32, A:A.275 Salt bridges: B:R.33, A:K.246, A:D.278, A:D.281 MES.3: 10 residues within 4Å: Chain A: K.30, F.31, E.32, R.33 Chain B: K.246, W.274, A.275, Y.276, D.278, D.281 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.30 Water bridges: A:R.33 Salt bridges: A:E.32, 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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