SMTL ID : 1xoe.2 (1 other biounit)

N9 Tern influenza neuraminidase complexed with (2R,4R,5R)-5-(1-Acetylamino-3-methyl-butyl-pyrrolidine-2, 4-dicarobyxylic acid 4-methyl esterdase complexed with

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.1: 21 residues within 4Å: Chain A: N.118, N.119, R.139 Chain C: R.246, N.248, D.249, R.282, I.284, I.286, E.293, L.295, K.307, P.308, T.309, Q.310, G.311, F.371, L.372, G.373, Q.374 Ligands: MAN.2 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.309, C:R.246, C:R.246, C:N.248, C:D.249, C:I.284, C:G.311, C:G.311 Water bridges: C:D.249, C:Q.310, C:Q.310, C:Q.374 Hydrophobic interactions: C:F.371 NAG-NAG-BMA-MAN-MAN-MAN.6: 21 residues within 4Å: Chain B: N.118, N.119, R.139 Chain D: R.246, N.248, D.249, R.282, I.284, I.286, E.293, L.295, K.307, P.308, T.309, Q.310, G.311, F.371, L.372, G.373, Q.374 Ligands: MAN.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.309, D:R.246, D:R.246, D:N.248, D:D.249, D:I.284, D:G.311, D:G.311 Water bridges: D:D.249, D:Q.310, D:Q.310, D:Q.374 Hydrophobic interactions: D:F.371 NAG-NAG-BMA-MAN-MAN-MAN.11: 21 residues within 4Å: Chain B: R.246, N.248, D.249, R.282, I.284, I.286, E.293, L.295, K.307, P.308, T.309, Q.310, G.311, F.371, L.372, G.373, Q.374 Chain C: N.118, N.119, R.139 Ligands: MAN.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.309, B:R.246, B:R.246, B:N.248, B:D.249, B:I.284, B:G.311, B:G.311 Water bridges: B:D.249, B:Q.310, B:Q.310, B:Q.374 Hydrophobic interactions: B:F.371 NAG-NAG-BMA-MAN-MAN-MAN.16: 21 residues within 4Å: Chain A: R.246, N.248, D.249, R.282, I.284, I.286, E.293, L.295, K.307, P.308, T.309, Q.310, G.311, F.371, L.372, G.373, Q.374 Chain D: N.118, N.119, R.139 Ligands: MAN.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.309, A:R.246, A:R.246, A:N.248, A:D.249, A:I.284, A:G.311, A:G.311 Water bridges: A:D.249, A:Q.310, A:Q.310, A:Q.374 Hydrophobic interactions: A:F.371

4 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.2: 2 residues within 4Å: Chain C: T.309 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP) MAN.7: 2 residues within 4Å: Chain D: T.309 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) MAN.12: 2 residues within 4Å: Chain B: T.309 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 No protein-ligand interaction detected (PLIP) MAN.17: 2 residues within 4Å: Chain A: T.309 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP)

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.3: 2 residues within 4Å: Chain A: N.64, W.356 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.64 NAG.4: 4 residues within 4Å: Chain A: D.1, F.2, N.4, N.153 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.1 Hydrogen bonds: A:D.1, A:F.2 Water bridges: A:N.4, A:N.4, A:N.4 NAG.8: 2 residues within 4Å: Chain B: N.64, W.356 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.64 NAG.9: 4 residues within 4Å: Chain B: D.1, F.2, N.4, N.153 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.1 Hydrogen bonds: B:D.1, B:F.2 Water bridges: B:N.4, B:N.4, B:N.4 NAG.13: 2 residues within 4Å: Chain C: N.64, W.356 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.64 NAG.14: 4 residues within 4Å: Chain C: D.1, F.2, N.4, N.153 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:D.1 Hydrogen bonds: C:D.1, C:F.2 Water bridges: C:N.4, C:N.4, C:N.4 NAG.18: 2 residues within 4Å: Chain D: N.64, W.356 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.64 NAG.19: 4 residues within 4Å: Chain D: D.1, F.2, N.4, N.153 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:D.1 Hydrogen bonds: D:D.1, D:F.2 Water bridges: D:N.4, D:N.4, D:N.4

4 x ABX: 5-[1-(ACETYLAMINO)-3-METHYLBUTYL]-4-(METHOXYCARBONYL)PROLINE(Non-covalent)

ABX.5: 15 residues within 4Å: Chain A: R.36, E.37, L.52, D.69, R.70, R.74, W.97, R.143, E.146, A.165, E.195, E.196, R.211, R.289, Y.323 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.97, A:E.195 Hydrogen bonds: A:E.37, A:R.70, A:E.146, A:E.196, A:Y.323 Water bridges: A:N.265 Salt bridges: A:R.36, A:R.211, A:R.289 ABX.10: 15 residues within 4Å: Chain B: R.36, E.37, L.52, D.69, R.70, R.74, W.97, R.143, E.146, A.165, E.195, E.196, R.211, R.289, Y.323 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.97, B:E.195 Hydrogen bonds: B:E.37, B:R.70, B:E.146, B:E.196, B:Y.323 Water bridges: B:N.265 Salt bridges: B:R.36, B:R.211, B:R.289 ABX.15: 15 residues within 4Å: Chain C: R.36, E.37, L.52, D.69, R.70, R.74, W.97, R.143, E.146, A.165, E.195, E.196, R.211, R.289, Y.323 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.97, C:E.195 Hydrogen bonds: C:E.37, C:R.70, C:E.146, C:E.196, C:Y.323 Water bridges: C:N.265 Salt bridges: C:R.36, C:R.211, C:R.289 ABX.20: 15 residues within 4Å: Chain D: R.36, E.37, L.52, D.69, R.70, R.74, W.97, R.143, E.146, A.165, E.195, E.196, R.211, R.289, Y.323 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.97, D:E.195 Hydrogen bonds: D:E.37, D:R.70, D:E.146, D:E.196, D:Y.323 Water bridges: D:N.265 Salt bridges: D:R.36, D:R.211, D:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, G.T. et al., Design, synthesis, and structural analysis of inhibitors of influenza neuraminidase containing a 2,3-disubstituted tetrahydrofuran-5-carboxylic acid core. Bioorg.Med.Chem.Lett. (2005)

Release Date

2005-01-11

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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