SMTL ID : 5w92.2 (1 other biounit)

Crystal structure of the influenza virus PA endonuclease in complex with an inhibitor - SRI-30049

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 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, KU0.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, 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, KU0.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1, H2O.1 MN.5: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.6, KU0.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.6: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.5, KU0.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.1, H2O.1 MN.9: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.10, KU0.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.10: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.9, KU0.11 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.2, H2O.2 MN.13: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.14, KU0.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.14: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.13, KU0.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.2, H2O.2

4 x KU0: 2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-[2-(phenylsulfonyl)ethyl]-1,6-dihydropyrimidine-4-carboxamide(Non-covalent)

KU0.3: 14 residues within 4Å: Chain A: Y.44, K.54, I.58, H.61, E.81, F.106, L.107, D.109, E.120, I.121, K.135, K.138 Ligands: MN.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.58, A:K.138 Hydrogen bonds: A:Y.44, A:Y.44, A:K.54, A:K.135, A:K.135 pi-Stacking: A:H.61, A:H.61 KU0.7: 14 residues within 4Å: Chain B: Y.44, K.54, I.58, H.61, E.81, F.106, L.107, D.109, E.120, I.121, K.135, K.138 Ligands: MN.5, MN.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.58, B:K.138 Hydrogen bonds: B:Y.44, B:Y.44, B:K.54, B:K.135, B:K.135 pi-Stacking: B:H.61, B:H.61 KU0.11: 14 residues within 4Å: Chain C: Y.44, K.54, I.58, H.61, E.81, F.106, L.107, D.109, E.120, I.121, K.135, K.138 Ligands: MN.9, MN.10 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.58, C:K.138 Hydrogen bonds: C:Y.44, C:Y.44, C:K.54, C:K.135, C:K.135 pi-Stacking: C:H.61, C:H.61 KU0.15: 14 residues within 4Å: Chain D: Y.44, K.54, I.58, H.61, E.81, F.106, L.107, D.109, E.120, I.121, K.135, K.138 Ligands: MN.13, MN.14 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.58, D:K.138 Hydrogen bonds: D:Y.44, D:Y.44, D:K.54, D:K.135, D:K.135 pi-Stacking: D:H.61, D:H.61

4 x 9HD: 1-[(3R,5S,7R)-1,5,7,9-tetrakis(2-oxopyrrolidin-1-yl)nonan-3-yl]-1,3-dihydro-2H-pyrrol-2-one(Non-covalent)

9HD.4: 7 residues within 4Å: Chain A: N.30, M.32, L.36, F.66, I.79, E.81, G.82 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.36, A:F.66, A:F.66, A:F.66, A:I.79 Hydrogen bonds: A:N.30 9HD.8: 7 residues within 4Å: Chain B: N.30, M.32, L.36, F.66, I.79, E.81, G.82 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.36, B:F.66, B:F.66, B:F.66, B:I.79 Hydrogen bonds: B:N.30 9HD.12: 7 residues within 4Å: Chain C: N.30, M.32, L.36, F.66, I.79, E.81, G.82 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.36, C:F.66, C:F.66, C:F.66, C:I.79 Hydrogen bonds: C:N.30 9HD.16: 7 residues within 4Å: Chain D: N.30, M.32, L.36, F.66, I.79, E.81, G.82 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.36, D:F.66, D:F.66, D:F.66, D:I.79 Hydrogen bonds: D:N.30

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

2018-02-07

Peptides

Polymerase acidic protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Polymerase acidic protein

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