SMTL ID : 5w9g.2 (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

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, 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 MN.6: 6 residues within 4Å: Chain B: H.61, D.109, E.120, I.121 Ligands: MN.7, KU2.9 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.61, B:D.109, 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, KU2.9 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.11: 6 residues within 4Å: Chain C: H.61, D.109, E.120, I.121 Ligands: MN.12, KU2.14 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.61, C:D.109, C:D.109, C:E.120, C:I.121 MN.12: 5 residues within 4Å: Chain C: H.61, E.81, D.109 Ligands: MN.11, KU2.14 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.16: 6 residues within 4Å: Chain D: H.61, D.109, E.120, I.121 Ligands: MN.17, KU2.19 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.61, D:D.109, D:D.109, D:E.120, D:I.121 MN.17: 5 residues within 4Å: Chain D: H.61, E.81, D.109 Ligands: MN.16, KU2.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.81, D:D.109, H2O.3, H2O.3

4 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 CL.8: 3 residues within 4Å: Chain B: S.73, R.76, K.114 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: S.73, R.76, K.114 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain D: S.73, R.76, K.114 Ligand excluded by PLIP

4 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 KU2.9: 14 residues within 4Å: Chain B: 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.6, MN.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.44, B:E.46, B:A.57, B:H.61 Hydrogen bonds: B:Y.131, B:Y.131 pi-Stacking: B:Y.44 KU2.14: 14 residues within 4Å: Chain C: 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.11, MN.12 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.44, C:E.46, C:A.57, C:H.61 Hydrogen bonds: C:Y.131, C:Y.131 pi-Stacking: C:Y.44 KU2.19: 14 residues within 4Å: Chain D: 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.16, MN.17 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.44, D:E.46, D:A.57, D:H.61 Hydrogen bonds: D:Y.131, D:Y.131 pi-Stacking: D:Y.44

4 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 SO4.10: 6 residues within 4Å: Chain B: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.51, B:E.51, B:N.53, B:N.53, B:K.54, B:S.195 SO4.15: 6 residues within 4Å: Chain C: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.51, C:E.51, C:N.53, C:N.53, C:K.54, C:S.195 SO4.20: 6 residues within 4Å: Chain D: I.50, E.51, T.52, N.53, K.54, S.195 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.51, D:E.51, D:N.53, D:N.53, D:K.54, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Polymerase acidic protein

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