SMTL ID : 5wef.1

Crystal structure of the influenza virus PA endonuclease (F105S mutant) in complex with inhibitor 7a (SRI-29770)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.41, D.89, E.100, I.101 Ligands: MN.2, GY6.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.41, A:D.89, A:E.100, A:I.101 MN.2: 5 residues within 4Å: Chain A: H.41, E.61, D.89 Ligands: MN.1, GY6.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:D.89, H2O.1, H2O.1

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)

GY6.3: 15 residues within 4Å: Chain A: A.20, Y.24, E.26, K.34, I.38, H.41, E.61, D.89, E.100, I.101, Y.111, K.115 Ligands: MN.1, MN.2, NA.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.20, A:Y.24, A:Y.24 Hydrogen bonds: A:Y.111, A:K.115

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

EDO.4: 5 residues within 4Å: Chain A: R.6, Q.7, F.9, N.10, P.11 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.9, A:N.10 EDO.5: 4 residues within 4Å: Chain A: E.15, E.18, K.19, K.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.18, A:E.18, A:K.22 Water bridges: A:E.15 EDO.6: 3 residues within 4Å: Chain A: F.46, G.62, R.63 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Ligands: GY6.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.87, A:E.100

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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