SMTL ID : 5we9.2 (1 other biounit)

Crystal structure of the influenza virus PA endonuclease in complex with inhibitor 7b (SRI-29731)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

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: MG.2, GY7.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.41, A:D.89, A:E.100, A:I.101 MN.5: 6 residues within 4Å: Chain B: H.41, D.89, E.100, I.101 Ligands: MG.6, GY7.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.41, B:D.89, B:E.100, B:I.101

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: H.41, E.61, D.89 Ligands: MN.1, GY7.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:D.89, H2O.1, H2O.3 MG.6: 5 residues within 4Å: Chain B: H.41, E.61, D.89 Ligands: MN.5, GY7.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.61, B:D.89, H2O.6, H2O.8

2 x GY7: 2-[(2S)-1-(2,6-difluorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

GY7.3: 11 residues within 4Å: Chain A: Y.24, I.38, H.41, E.61, D.89, E.100, I.101, K.115, K.118 Ligands: MN.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.24, A:H.41 Hydrogen bonds: A:K.115 Water bridges: A:I.101, A:Y.111 pi-Stacking: A:H.41 GY7.7: 11 residues within 4Å: Chain B: Y.24, I.38, H.41, E.61, D.89, E.100, I.101, K.115, K.118 Ligands: MN.5, MG.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.24, B:Y.24, B:H.41 Hydrogen bonds: B:K.115 Water bridges: B:I.101, B:Y.111 pi-Stacking: B:H.41

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

EDO.4: 7 residues within 4Å: Chain A: P.84, F.86, L.87, P.88, E.100, I.119, T.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.100, A:T.124 EDO.8: 7 residues within 4Å: Chain B: P.84, F.86, L.87, P.88, E.100, I.119, T.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Polymerase acidic protein

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