SMTL ID : 4m5o.1 (1 other biounit)

3-HYDROXY-6-PHENYL-1,2-DIHYDROPYRIDIN-2-ONE bound to influenza 2009 H1N1 endonuclease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: H.78, D.145, E.156, I.157 Ligands: MN.2, X48.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.78, A:D.145, A:E.156, A:I.157, X48.6 MN.2: 6 residues within 4Å: Chain A: H.78, E.117, D.145 Ligands: MN.1, X48.6, X48.8 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.117, A:D.145, H2O.1, H2O.3, H2O.6 MN.3: 3 residues within 4Å: Chain A: E.117 Ligands: X48.7, X48.8 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:E.117, H2O.1, X48.7, X48.8

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: I.67, E.68, T.69, N.70 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.69, A:N.70, A:N.70 Water bridges: A:E.68

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

EDO.5: 7 residues within 4Å: Chain A: N.70, K.71, A.74, R.161, S.231, E.232 Ligands: X48.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.161, A:R.161, A:S.231 Water bridges: A:E.232, A:E.232

3 x X48: 3-hydroxy-6-phenylpyridin-2(5H)-one(Non-covalent)

X48.6: 13 residues within 4Å: Chain A: K.71, A.74, I.75, H.78, E.117, D.145, E.156, I.157, K.171 Ligands: MN.1, MN.2, EDO.5, X48.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.71, A:A.74, A:I.75 Hydrogen bonds: A:K.171 Water bridges: A:Y.167, A:Y.167 pi-Cation interactions: A:H.78 X48.7: 10 residues within 4Å: Chain A: K.56, A.57, E.60, Y.61, E.117, G.118, R.119, D.120 Ligands: MN.3, X48.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.56, A:K.56, A:E.60, A:Y.61, A:D.120 Hydrogen bonds: A:G.118 Water bridges: A:A.57, A:A.57, A:R.119 X48.8: 10 residues within 4Å: Chain A: A.57, Y.61, E.63, K.71, I.75, E.117 Ligands: MN.2, MN.3, X48.6, X48.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.61, A:E.63, A:K.71, A:I.75 pi-Stacking: A:Y.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauman, J.D. et al., Crystallographic fragment screening and structure-based optimization yields a new class of influenza endonuclease inhibitors. Acs Chem.Biol. (2013)

Release Date

2013-09-18

Peptides

Polymerase PA: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polymerase PA

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