SMTL ID : 5wei.1

Crystal structure of the influenza virus PA endonuclease (E119D mutant) in complex with inhibitor 7a (SRI-29770)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.61, D.109, D.120, I.121 Ligands: MN.2, GY6.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:D.120, A:I.121 MN.2: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.1, GY6.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1, H2O.1

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

SO4.3: 4 residues within 4Å: Chain A: E.51, T.52, N.53, K.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.51, A:T.52, A:N.53, A:N.53, A:K.54 SO4.4: 4 residues within 4Å: Chain A: G.72, S.73, R.76, K.114 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.73, A:S.73, A:S.73 Salt bridges: A:R.76, A:K.114 SO4.5: 3 residues within 4Å: Chain A: R.83, D.84, M.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.84, A:D.84 Salt bridges: A:R.83

1 x GY6: 2-[(2S)-1-(2,6-dichlorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

GY6.6: 11 residues within 4Å: Chain A: Y.44, K.54, I.58, H.61, E.81, D.109, D.120, I.121, Y.131 Ligands: MN.1, MN.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.44 Hydrogen bonds: A:Y.131, A:Y.131 pi-Stacking: A:H.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beylkin, D. et al., Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep (2017)

Release Date

2017-12-27

Peptides

Polymerase acidic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polymerase acidic protein

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