SMTL ID : 8k9x.1

Crystal structure of plasmodium LysRS complexing with ASP3026 derived LysRS inhibitor 5 (ADKI5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x JUA: (2~{S})-2,6-bis(azanyl)-~{N}-[3-[2-[[4-[(2,5-dimethoxyphenyl)amino]-1,3,5-triazin-2-yl]amino]phenyl]sulfonylpropyl]hexanamide(Non-covalent)

JUA.1: 25 residues within 4Å: Chain A: A.231, E.233, R.255, E.257, G.258, T.262, H.263, N.264, P.265, F.267, E.271, Y.273, E.425, V.426, L.427, N.428, Y.430, E.432, G.477, L.478, G.479, L.480, G.481, R.484, I.495 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.255, A:E.257, A:F.267 Hydrogen bonds: A:E.233, A:R.255, A:N.264, A:N.264, A:N.428, A:E.432 pi-Stacking: A:H.263, A:F.267 JUA.4: 23 residues within 4Å: Chain B: E.233, R.255, E.257, G.258, T.262, H.263, N.264, P.265, F.267, E.271, Y.273, E.425, V.426, L.427, N.428, Y.430, E.432, G.477, L.478, G.479, G.481, R.484, I.495 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:R.255, B:E.257, B:E.257, B:E.425, B:Y.430 Hydrogen bonds: B:E.233, B:R.255, B:R.255, B:N.264, B:N.264, B:Y.273, B:N.428, B:E.432 pi-Stacking: B:H.263, B:F.267 pi-Cation interactions: B:R.255

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

MES.2: 9 residues within 4Å: Chain A: K.30, F.31, E.32, R.33 Chain B: K.246, W.274, Y.276, D.278, D.281 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.246, B:D.281, A:R.33 MES.3: 8 residues within 4Å: Chain A: W.274, Y.276, D.278, D.281 Chain B: K.30, F.31, E.32, R.33 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.274, B:K.30 Salt bridges: A:K.246, A:D.278, A:D.281, B:R.33

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