SMTL ID : 5w9g.1 (1 other biounit)

Crystal structure of the influenza virus PA endonuclease in complex with inhibitor 9k (SRI-30023)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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, E.120, I.121 Ligands: MN.2, KU2.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.61, A:D.109, A:D.109, A:E.120, A:I.121 MN.2: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.1, KU2.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1, H2O.1

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: S.73, R.76, K.114 Ligand excluded by PLIP

1 x KU2: 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-1,6-dihydropyrimidine-4 -carboxamide(Non-covalent)

KU2.4: 14 residues within 4Å: Chain A: A.40, M.41, Y.44, E.46, A.57, I.58, H.61, E.81, D.109, E.120, I.121, Y.131 Ligands: MN.1, MN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.44, A:E.46, A:A.57, A:H.61 Hydrogen bonds: A:Y.131, A:Y.131 pi-Stacking: A:Y.44

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

SO4.5: 6 residues within 4Å: Chain A: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.51, A:E.51, A:N.53, A:N.53, A:K.54, A:S.195

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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