SMTL ID : 7bt5.1

Crystal structure of plasmodium LysRS complexing with an antitumor compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 11 residues within 4Å: Chain A: A.231, E.233, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 Ligands: F6O.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.430 Hydrogen bonds: A:E.233, A:Y.273, A:N.428 LYS.3: 9 residues within 4Å: Chain B: E.233, E.271, Y.273, N.428, Y.430, E.432, G.477, L.478, G.479 6 PLIP interactions: 6 interactions with chain B, Hydrophobic interactions: B:N.428 Hydrogen bonds: B:E.233, B:E.233, B:Y.273, B:Y.273, B:N.428

2 x F6O: N4-[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N2-(2-propan-2-ylsulfonylphenyl)-1,3,5-triazine-2,4-diamine(Non-covalent)

F6O.2: 17 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, L.480, G.481, R.484, I.495 Ligands: LYS.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.425 Hydrogen bonds: A:N.264, A:N.264 Water bridges: A:G.481, A:D.483 pi-Stacking: A:H.263, A:F.267 F6O.4: 17 residues within 4Å: Chain B: N.211, A.212, 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 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.257, B:E.425 Hydrogen bonds: B:N.264, B:N.264 Water bridges: B:R.484 Salt bridges: B:D.260 pi-Stacking: B:H.263, B:F.267 pi-Cation interactions: B:H.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., Inhibition of Plasmodium falciparum Lysyl-tRNA synthetase via an anaplastic lymphoma kinase inhibitor. Nucleic Acids Res. (2020)

Release Date

2020-09-30

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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