SMTL ID : 6yks.1

Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x OVT: [(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-[4-(2-phenylethyl)-1,2,3-triazol-1-yl]propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate(Non-covalent)

OVT.1: 23 residues within 4Å: Chain A: M.41, F.42, P.43, Y.44, H.50, G.52, H.53, N.56, Y.57, D.81, S.511, Y.514, Y.542, G.544, G.545, E.547, H.548, H.552, Q.581, M.583, V.584, K.635, M.636 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.41, A:F.42, A:H.50, A:M.636 Hydrogen bonds: A:F.42, A:Y.44, A:D.81, A:G.545, A:E.547, A:V.584 Water bridges: A:E.547 Salt bridges: A:H.53

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.450, C.453, C.491, C.494 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.450, A:C.453, A:C.491, A:C.494

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: T.197, R.431, D.432 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.432 Water bridges: A:L.430, A:R.431 EDO.4: 5 residues within 4Å: Chain A: W.224, E.302, Y.340, R.429, L.430 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.224, A:Y.340, A:Y.340 Water bridges: A:R.431, A:R.431 EDO.5: 6 residues within 4Å: Chain A: W.224, L.430, R.431, D.432, W.433, Y.555 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.224, A:Y.555 Water bridges: A:D.432, A:G.434

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: E.211 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Ruysscher, D. et al., Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors. Eur.J.Med.Chem. (2021)

Release Date

2020-12-02

Peptides

Leucine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Leucine--tRNA ligase

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