SMTL ID : 7k87.1

The crystal structure of the 2009 H1N1 PA endonuclease in complex with SJ000986436

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-octamer

Ligands

8 x QQ4: Hexa Vinylpyrrolidone K15(Non-covalent)

QQ4.1: 4 residues within 4Å: Chain A: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.66, A:F.66, A:I.79, A:I.79 Water bridges: A:R.83 QQ4.5: 4 residues within 4Å: Chain B: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.66, B:F.66, B:I.79, B:I.79 Water bridges: B:R.83 QQ4.9: 4 residues within 4Å: Chain C: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.66, C:F.66, C:I.79, C:I.79 Water bridges: C:R.83 QQ4.13: 4 residues within 4Å: Chain D: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.66, D:F.66, D:I.79, D:I.79 Water bridges: D:R.83 QQ4.17: 4 residues within 4Å: Chain E: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.66, E:F.66, E:I.79, E:I.79 Water bridges: E:R.83 QQ4.21: 4 residues within 4Å: Chain F: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.66, F:F.66, F:I.79, F:I.79 Water bridges: F:R.83 QQ4.25: 4 residues within 4Å: Chain G: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:F.66, G:F.66, G:I.79, G:I.79 Water bridges: G:R.83 QQ4.29: 4 residues within 4Å: Chain H: M.32, F.66, I.79, E.81 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:F.66, H:F.66, H:I.79, H:I.79 Water bridges: H:R.83

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

MN.2: 6 residues within 4Å: Chain A: H.61, D.109, E.120, I.121 Ligands: MN.3, W5V.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:D.109, A:E.120, A:I.121 MN.3: 5 residues within 4Å: Chain A: H.61, E.81, D.109 Ligands: MN.2, W5V.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.81, A:D.109, H2O.1 MN.6: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.7, W5V.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:D.109, B:E.120, B:I.121 MN.7: 5 residues within 4Å: Chain B: H.61, E.81, D.109 Ligands: MN.6, W5V.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.81, B:D.109, H2O.2 MN.10: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.11, W5V.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:D.109, C:E.120, C:I.121 MN.11: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.10, W5V.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.81, C:D.109, H2O.4 MN.14: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.15, W5V.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:D.109, D:E.120, D:I.121 MN.15: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.14, W5V.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.5 MN.18: 6 residues within 4Å: Chain E: H.61, D.109, E.120, I.121 Ligands: MN.19, W5V.20 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.61, E:D.109, E:E.120, E:I.121 MN.19: 5 residues within 4Å: Chain E: H.61, E.81, D.109 Ligands: MN.18, W5V.20 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.81, E:D.109, H2O.7 MN.22: 6 residues within 4Å: Chain F: H.61, D.109, E.120, I.121 Ligands: MN.23, W5V.24 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.61, F:D.109, F:E.120, F:I.121 MN.23: 5 residues within 4Å: Chain F: H.61, E.81, D.109 Ligands: MN.22, W5V.24 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.81, F:D.109, H2O.9 MN.26: 6 residues within 4Å: Chain G: H.61, D.109, E.120, I.121 Ligands: MN.27, W5V.28 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.61, G:D.109, G:E.120, G:I.121 MN.27: 5 residues within 4Å: Chain G: H.61, E.81, D.109 Ligands: MN.26, W5V.28 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:E.81, G:D.109, H2O.10 MN.30: 6 residues within 4Å: Chain H: H.61, D.109, E.120, I.121 Ligands: MN.31, W5V.32 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.61, H:D.109, H:E.120, H:I.121 MN.31: 5 residues within 4Å: Chain H: H.61, E.81, D.109 Ligands: MN.30, W5V.32 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.81, H:D.109, H2O.12

8 x W5V: 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide(Non-covalent)

W5V.4: 16 residues within 4Å: Chain A: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.2, MN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.40, A:K.54 Hydrogen bonds: A:K.135 Water bridges: A:V.123 pi-Stacking: A:Y.44 pi-Cation interactions: A:H.61 W5V.8: 16 residues within 4Å: Chain B: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.6, MN.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.40, B:K.54 Hydrogen bonds: B:K.135 Water bridges: B:V.123 pi-Stacking: B:Y.44 pi-Cation interactions: B:H.61 W5V.12: 16 residues within 4Å: Chain C: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.10, MN.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.40, C:K.54 Hydrogen bonds: C:K.135 Water bridges: C:V.123 pi-Stacking: C:Y.44 pi-Cation interactions: C:H.61 W5V.16: 16 residues within 4Å: Chain D: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.14, MN.15 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.40, D:K.54 Hydrogen bonds: D:K.135 Water bridges: D:E.81, D:V.123 pi-Stacking: D:Y.44 pi-Cation interactions: D:H.61 W5V.20: 16 residues within 4Å: Chain E: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.18, MN.19 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.40, E:K.54 Hydrogen bonds: E:Y.131, E:K.135 Water bridges: E:V.123 pi-Stacking: E:Y.44 pi-Cation interactions: E:H.61 W5V.24: 16 residues within 4Å: Chain F: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.22, MN.23 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.40, F:K.54 Hydrogen bonds: F:Y.131, F:K.135 Water bridges: F:V.123 pi-Stacking: F:Y.44 pi-Cation interactions: F:H.61 W5V.28: 16 residues within 4Å: Chain G: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.26, MN.27 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:A.40, G:K.54 Hydrogen bonds: G:Y.131, G:K.135 Water bridges: G:V.123 pi-Stacking: G:Y.44 pi-Cation interactions: G:H.61 W5V.32: 16 residues within 4Å: Chain H: A.40, M.41, Y.44, E.46, K.54, H.61, E.81, L.107, D.109, E.120, I.121, G.122, Y.131, K.135 Ligands: MN.30, MN.31 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:A.40, H:K.54 Hydrogen bonds: H:Y.131, H:K.135 Water bridges: H:V.123 pi-Stacking: H:Y.44 pi-Cation interactions: H:H.61

Links

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Citation

Slavish, P.J. et al., Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Eur.J.Med.Chem. (2023)

Release Date

2021-09-29

Peptides

Protein PA-X: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Protein PA-X

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