SMTL ID : 5zh4.1

CRYSTAL STRUCTURE OF PfKRS WITH INHIBITOR CLADO-7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 14 residues within 4Å: Chain A: G.208, A.209, A.230, E.232, R.254, E.270, Y.272, N.427, A.428, Y.429, E.431, G.476, G.478 Ligands: 9CC.2 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:Y.429 Hydrogen bonds: A:G.208, A:E.232, A:E.270, A:Y.272, A:N.427, A:E.431 Salt bridges: A:R.254 LYS.5: 13 residues within 4Å: Chain B: G.208, A.209, A.230, E.232, R.254, E.270, Y.272, N.427, Y.429, E.431, G.476, G.478 Ligands: 9CC.6 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:G.208, B:E.270, B:Y.272, B:N.427, K.5 Salt bridges: B:R.254

2 x 9CC: (3R)-6,8-dihydroxy-3-{[(2S,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one(Non-covalent)

9CC.2: 17 residues within 4Å: Chain A: R.254, E.256, T.261, H.262, N.263, F.266, S.268, E.424, V.425, L.426, N.427, G.478, L.479, G.480, R.483, I.494 Ligands: LYS.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.262, A:F.266, A:E.424 Hydrogen bonds: A:R.254, A:E.256, A:E.256, A:N.263, A:N.263 Salt bridges: A:R.483 pi-Stacking: A:H.262, A:F.266 9CC.6: 14 residues within 4Å: Chain B: R.254, E.256, T.261, H.262, N.263, F.266, E.424, V.425, L.426, N.427, G.478, R.483, I.494 Ligands: LYS.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.424 Hydrogen bonds: B:E.256, B:N.263, B:N.263 Salt bridges: B:R.483 pi-Stacking: B:H.262, B:F.266

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: N.279, R.407 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: H.262, R.483 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: N.279, R.407 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: H.262, R.483 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.32 Chain B: W.273 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, P. et al., Specific Stereoisomeric Conformations Determine the Drug Potency of Cladosporin Scaffold against Malarial Parasite. J. Med. Chem. (2018)

Release Date

2018-06-27

Peptides

Lysine-tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-tRNA ligase

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