SMTL ID : 5jyy.1

Structure-based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-resistant Influenza Viruses

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 18 residues within 4Å: Chain A: N.119, N.120 Chain C: R.247, N.249, D.250, R.283, I.285, T.287, E.294, L.296, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 4 PLIP interactions: 4 interactions with chain C Water bridges: C:G.312, C:Q.311, C:Q.311 Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 18 residues within 4Å: Chain B: N.119, N.120 Chain D: R.247, N.249, D.250, R.283, I.285, T.287, E.294, L.296, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 4 PLIP interactions: 4 interactions with chain D Water bridges: D:G.312, D:Q.311, D:Q.311 Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11: 18 residues within 4Å: Chain B: R.247, N.249, D.250, R.283, I.285, T.287, E.294, L.296, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120 4 PLIP interactions: 4 interactions with chain B Water bridges: B:G.312, B:Q.311, B:Q.311 Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.16: 18 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, T.287, E.294, L.296, P.309, I.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.312, A:Q.311, A:Q.311 Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: N.2, F.3, N.5, N.154 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.2 Hydrogen bonds: A:N.2, A:F.3, A:N.5 NAG.3: 2 residues within 4Å: Chain A: N.65, W.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65, A:W.357 NAG.7: 4 residues within 4Å: Chain B: N.2, F.3, N.5, N.154 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.2 Hydrogen bonds: B:N.2, B:F.3, B:N.5 NAG.8: 2 residues within 4Å: Chain B: N.65, W.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.65, B:W.357 NAG.12: 4 residues within 4Å: Chain C: N.2, F.3, N.5, N.154 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.2 Hydrogen bonds: C:N.2, C:F.3, C:N.5 NAG.13: 2 residues within 4Å: Chain C: N.65, W.357 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.65, C:W.357 NAG.17: 4 residues within 4Å: Chain D: N.2, F.3, N.5, N.154 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.2 Hydrogen bonds: D:N.2, D:F.3, D:N.5 NAG.18: 2 residues within 4Å: Chain D: N.65, W.357 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.65, D:W.357

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.213, G.217, D.244, N.266, G.267 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.213, A:G.217, A:D.244, A:N.266, H2O.5, H2O.6 CA.9: 5 residues within 4Å: Chain B: D.213, G.217, D.244, N.266, G.267 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.213, B:G.217, B:D.244, B:N.266, H2O.19, H2O.20 CA.14: 5 residues within 4Å: Chain C: D.213, G.217, D.244, N.266, G.267 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.213, C:G.217, C:D.244, C:N.266, H2O.34, H2O.35 CA.19: 5 residues within 4Å: Chain D: D.213, G.217, D.244, N.266, G.267 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.213, D:G.217, D:D.244, D:N.266, H2O.48, H2O.49

4 x 6PY: 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-enon ic acid(Non-covalent)

6PY.5: 15 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142 Hydrogen bonds: A:R.71, A:W.98, A:W.98, A:R.144, A:E.197, A:K.212 Water bridges: A:R.37, A:D.70, A:D.70, A:R.75, A:R.144, A:E.147, A:E.197, A:K.212, A:R.290 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.290 6PY.10: 15 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142 Hydrogen bonds: B:R.71, B:W.98, B:W.98, B:R.144, B:E.197, B:K.212 Water bridges: B:R.37, B:D.70, B:D.70, B:R.75, B:R.144, B:E.147, B:E.197, B:K.212, B:R.290 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.290 6PY.15: 15 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142 Hydrogen bonds: C:R.71, C:W.98, C:W.98, C:R.144, C:E.197, C:K.212 Water bridges: C:R.37, C:D.70, C:D.70, C:R.75, C:R.144, C:E.147, C:E.197, C:K.212, C:R.290 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.290 6PY.20: 15 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, R.75, W.98, I.142, R.144, E.147, A.166, E.196, E.197, K.212, R.290, Y.324 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142 Hydrogen bonds: D:R.71, D:W.98, D:W.98, D:R.144, D:E.197, D:K.212 Water bridges: D:R.37, D:D.70, D:D.70, D:R.75, D:R.144, D:E.147, D:E.197, D:K.212, D:R.290 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, L. et al., Structure-Based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-Resistant Influenza Viruses. J.Med.Chem. (2016)

Release Date

2016-06-29

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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