- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.92 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LYS: LYSINE(Non-covalent)
- 2 x D4X: (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydro-2~{H}-isoquinolin-1-one(Non-covalent)
D4X.2: 15 residues within 4Å:- Chain A: R.255, E.257, T.262, H.263, N.264, F.267, S.269, E.425, V.426, L.427, N.428, G.479, R.484, I.495
- Ligands: LYS.1
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:H.263, A:F.267, A:E.425, A:N.428
- Hydrogen bonds: A:E.257, A:N.264, A:N.264
- Water bridges: A:N.264
- pi-Stacking: A:H.263, A:F.267
D4X.7: 17 residues within 4Å:- Chain B: R.255, E.257, T.262, H.263, N.264, F.267, S.269, E.425, V.426, L.427, N.428, G.479, L.480, G.481, R.484, I.495
- Ligands: LYS.6
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:H.263, B:F.267, B:E.425
- Hydrogen bonds: B:E.257, B:N.264, B:N.264, B:R.484
- Water bridges: B:N.264, B:D.483, B:D.483
- pi-Stacking: B:H.263, B:F.267
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 7 residues within 4Å:- Chain A: K.246, W.274, A.275, Y.276
- Chain B: K.30, E.32, R.33
12 PLIP interactions:9 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:K.30, B:K.30, A:K.246, A:K.246
- Water bridges: B:K.30, B:E.32, B:R.33, B:R.33, B:R.33, B:R.33, B:R.33, A:Y.276
GOL.4: 7 residues within 4Å:- Chain A: I.183, R.187, I.250
- Chain B: R.187, E.197, E.199
- Ligands: GOL.9
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:R.187, B:R.187, A:R.187, A:R.187, A:I.250
GOL.5: 5 residues within 4Å:- Chain A: Y.279, N.280, H.407, R.408, E.415
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.280, A:E.395, A:R.408
- Water bridges: A:N.280
GOL.8: 8 residues within 4Å:- Chain A: K.30, E.32, R.33
- Chain B: K.246, W.274, A.275, Y.276, A.277
11 PLIP interactions:9 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:K.30, A:K.30, A:R.33, B:K.246, B:K.246
- Water bridges: A:E.32, A:R.33, A:R.33, A:R.33, A:R.33, A:R.33
GOL.9: 7 residues within 4Å:- Chain A: R.187, E.197, E.199
- Chain B: I.183, R.187, I.250
- Ligands: GOL.4
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:R.187, B:R.187, B:I.250, A:R.187, A:R.187, A:E.199
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhou, J. et al., Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase. Acs Chem.Biol. (2020)
- Release Date
- 2020-04-08
- Peptides
- Lysine--tRNA ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.92 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x LYS: LYSINE(Non-covalent)
- 2 x D4X: (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydro-2~{H}-isoquinolin-1-one(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhou, J. et al., Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase. Acs Chem.Biol. (2020)
- Release Date
- 2020-04-08
- Peptides
- Lysine--tRNA ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
B