SMTL ID : 1l7f.1

Crystal structure of influenza virus neuraminidase in complex with BCX-1812

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.1: 20 residues within 4Å: Chain A: N.119, N.120, R.140 Chain C: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.312, C:Q.313, C:Q.311, C:G.312 Hydrophobic interactions: C:F.372 Hydrogen bonds: C:G.312, C:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.10: 20 residues within 4Å: Chain B: N.119, N.120, R.140 Chain D: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 5 PLIP interactions: 5 interactions with chain D Water bridges: D:G.312, D:Q.313, D:Q.311, D:G.312 Hydrophobic interactions: D:F.372 Hydrogen bonds: D:G.312, D:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 20 residues within 4Å: Chain B: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain C: N.119, N.120, R.140 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.312, B:Q.313, B:Q.311, B:G.312 Hydrophobic interactions: B:F.372 Hydrogen bonds: B:G.312, B:Q.375 NAG-NAG-BMA-MAN-MAN-MAN-MAN.28: 20 residues within 4Å: Chain A: R.247, N.249, D.250, R.283, I.285, I.287, E.294, L.296, K.308, P.309, T.310, Q.311, G.312, F.372, L.373, G.374, Q.375 Chain D: N.119, N.120, R.140 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.312, A:Q.313, A:Q.311, A:G.312 Hydrophobic interactions: A:F.372 Hydrogen bonds: A:G.312, A:Q.375

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.2 Water bridges: A:D.2, A:N.154 NAG-NAG.11: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.2 Water bridges: B:D.2, B:N.154 NAG-NAG.20: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.2 Water bridges: C:D.2, C:N.154 NAG-NAG.29: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.2 Water bridges: D:D.2, D:N.154

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

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.12: 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.21: 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.30: 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

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 5 residues within 4Å: Chain A: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.217, A:D.244, A:N.266, H2O.2, H2O.5 CA.5: 3 residues within 4Å: Ligands: CA.14, CA.23, CA.32 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain B: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.217, B:D.244, B:N.266, H2O.27, H2O.30 CA.14: 3 residues within 4Å: Ligands: CA.5, CA.23, CA.32 No protein-ligand interaction detected (PLIP) CA.22: 5 residues within 4Å: Chain C: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.217, C:D.244, C:N.266, H2O.52, H2O.54 CA.23: 3 residues within 4Å: Ligands: CA.5, CA.14, CA.32 No protein-ligand interaction detected (PLIP) CA.31: 5 residues within 4Å: Chain D: D.213, G.217, D.244, N.266, G.267 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.217, D:D.244, D:N.266, H2O.77, H2O.79 CA.32: 3 residues within 4Å: Ligands: CA.5, CA.14, CA.23 No protein-ligand interaction detected (PLIP)

4 x BCZ: 3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID(Non-covalent)

BCZ.6: 15 residues within 4Å: Chain A: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, E.196, E.197, R.212, R.290, Y.324 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144, A:E.196 Hydrogen bonds: A:D.70, A:R.71, A:R.75, A:W.98 Water bridges: A:D.70, A:R.75, A:E.147, A:E.197, A:R.212 Salt bridges: A:R.37, A:E.38, A:D.70, A:E.147, A:R.212, A:R.290 BCZ.15: 15 residues within 4Å: Chain B: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, E.196, E.197, R.212, R.290, Y.324 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144, B:E.196 Hydrogen bonds: B:D.70, B:R.71, B:R.75, B:W.98 Water bridges: B:D.70, B:R.75, B:E.147, B:E.197, B:R.212 Salt bridges: B:R.37, B:E.38, B:D.70, B:E.147, B:R.212, B:R.290 BCZ.24: 15 residues within 4Å: Chain C: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, E.196, E.197, R.212, R.290, Y.324 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144, C:E.196 Hydrogen bonds: C:D.70, C:R.71, C:R.75, C:W.98 Water bridges: C:D.70, C:R.75, C:E.147, C:E.197, C:R.212 Salt bridges: C:R.37, C:E.38, C:D.70, C:E.147, C:R.212, C:R.290 BCZ.33: 15 residues within 4Å: Chain D: R.37, E.38, L.53, D.70, R.71, R.75, W.98, I.142, R.144, E.147, E.196, E.197, R.212, R.290, Y.324 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144, D:E.196 Hydrogen bonds: D:D.70, D:R.71, D:R.75, D:W.98 Water bridges: D:D.70, D:R.75, D:E.147, D:E.197, D:R.212 Salt bridges: D:R.37, D:E.38, D:D.70, D:E.147, D:R.212, D:R.290

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: K.255, C.256, N.257, D.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.256, A:N.257, A:D.258, A:D.305, A:D.305 GOL.8: 5 residues within 4Å: Chain A: H.63, N.65, S.72, Y.74 Chain C: R.26 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.63, C:R.26, C:R.26 Water bridges: A:S.72, A:S.72 GOL.9: 6 residues within 4Å: Chain A: C.11, A.333, E.334, G.335, C.337, R.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.339 Water bridges: A:E.336, A:R.339 GOL.16: 4 residues within 4Å: Chain B: K.255, C.256, N.257, D.258 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.256, B:N.257, B:D.258, B:D.305, B:D.305 GOL.17: 5 residues within 4Å: Chain B: H.63, N.65, S.72, Y.74 Chain D: R.26 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.63, D:R.26, D:R.26 Water bridges: B:S.72, B:S.72 GOL.18: 6 residues within 4Å: Chain B: C.11, A.333, E.334, G.335, C.337, R.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.339 Water bridges: B:E.336, B:R.339 GOL.25: 4 residues within 4Å: Chain C: K.255, C.256, N.257, D.258 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:C.256, C:N.257, C:D.258, C:D.305, C:D.305 GOL.26: 5 residues within 4Å: Chain B: R.26 Chain C: H.63, N.65, S.72, Y.74 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.26, B:R.26, C:H.63 Water bridges: C:S.72, C:S.72 GOL.27: 6 residues within 4Å: Chain C: C.11, A.333, E.334, G.335, C.337, R.339 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.339 Water bridges: C:E.336, C:R.339 GOL.34: 4 residues within 4Å: Chain D: K.255, C.256, N.257, D.258 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:C.256, D:N.257, D:D.258, D:D.305, D:D.305 GOL.35: 5 residues within 4Å: Chain A: R.26 Chain D: H.63, N.65, S.72, Y.74 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.63, A:R.26, A:R.26 Water bridges: D:S.72, D:S.72 GOL.36: 6 residues within 4Å: Chain D: C.11, A.333, E.334, G.335, C.337, R.339 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.339 Water bridges: D:E.336, D:R.339

Links

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Citation

Smith, B.J. et al., Structural studies of the resistance of influenza virus neuramindase to inhibitors. J.Med.Chem. (2002)

Release Date

2002-05-29

Peptides

neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

neuraminidase

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