SMTL ID : 5w3i.1

Crystal structure of the influenza virus PA endonuclease in complex with inhibitor 6e (SRI-29685)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: H.41, D.89, E.100, I.101, K.115 Ligands: MN.2, GY5.4 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, GY5.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:D.89, H2O.1, H2O.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: S.49, K.54, F.57, E.58, I.59 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.57

1 x GY5: 5-hydroxy-N-(2-methoxyethyl)-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

GY5.4: 12 residues within 4Å: Chain A: K.34, I.38, H.41, E.61, D.89, E.100, I.101, G.102, Y.111, K.115 Ligands: MN.1, MN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.38, A:H.41 Hydrogen bonds: A:K.34, A:D.89, A:Y.111, A:Y.111, A:K.115 pi-Stacking: A:H.41

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