SMTL ID : 5w2u.1

INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 7-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- 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)]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.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 Hydrogen bonds: C:G.312, C:G.312, C:Q.375 Hydrophobic interactions: C:F.372 Water bridges: C:Q.311, C:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.8: 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 Hydrogen bonds: D:G.312, D:G.312, D:Q.375 Hydrophobic interactions: D:F.372 Water bridges: D:Q.311, D:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.15: 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 Hydrogen bonds: B:G.312, B:G.312, B:Q.375 Hydrophobic interactions: B:F.372 Water bridges: B:Q.311, B:G.312 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.22: 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 Hydrogen bonds: A:G.312, A:G.312, A:Q.375 Hydrophobic interactions: A:F.372 Water bridges: A:Q.311, A:G.312

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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.154 NAG-NAG.9: 4 residues within 4Å: Chain B: D.2, F.3, N.5, N.154 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.154 NAG-NAG.16: 4 residues within 4Å: Chain C: D.2, F.3, N.5, N.154 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.154 NAG-NAG.23: 4 residues within 4Å: Chain D: D.2, F.3, N.5, N.154 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.154

4 x 9SM: (2R,3R,4R,5R,6S)-5-acetamido-6-[(2S)-2,3-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxane-2-carboxylic acid(Non-covalent)

9SM.3: 9 residues within 4Å: Chain A: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.321, A:W.321 Hydrogen bonds: A:S.286, A:S.289, A:S.291, A:S.291, A:N.318, A:N.318, A:K.352 9SM.10: 9 residues within 4Å: Chain B: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.321, B:W.321 Hydrogen bonds: B:S.286, B:S.289, B:S.291, B:S.291, B:N.318, B:N.318, B:K.352 9SM.17: 9 residues within 4Å: Chain C: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.321, C:W.321 Hydrogen bonds: C:S.286, C:S.289, C:S.291, C:S.291, C:N.318, C:N.318, C:K.352 9SM.24: 9 residues within 4Å: Chain D: S.286, A.288, S.289, S.291, N.318, T.319, D.320, W.321, K.352 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.321, D:W.321 Hydrogen bonds: D:S.286, D:S.289, D:S.291, D:S.291, D:N.318, D:N.318, D:K.352

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

NAG.4: 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.11: 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.18: 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.25: 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.5: 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:D.213, A:G.217, A:D.244, H2O.1, H2O.4 CA.12: 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:D.213, B:G.217, B:D.244, H2O.17, H2O.21 CA.19: 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:D.213, C:G.217, C:D.244, H2O.34, H2O.37 CA.26: 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:D.213, D:G.217, D:D.244, H2O.50, H2O.53

4 x 9S4: (2~{S},3~{R},4~{R},5~{R})-3-acetamido-2-[(2~{S})-2,3-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid(Non-covalent)

9S4.6: 14 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, R.290, Y.324 Ligands: 9SJ.7 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142 Hydrogen bonds: A:R.71, A:R.144, A:E.197, A:R.212, A:R.212 Water bridges: A:R.37, A:E.147, A:E.147, A:E.147, A:E.197 Salt bridges: A:R.37, A:R.212, A:R.290 Halogen bonds: A:D.70 9S4.13: 14 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, R.290, Y.324 Ligands: 9SJ.14 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142 Hydrogen bonds: B:R.71, B:R.144, B:E.197, B:R.212, B:R.212 Water bridges: B:R.37, B:E.147, B:E.147, B:E.147, B:E.197 Salt bridges: B:R.37, B:R.212, B:R.290 Halogen bonds: B:D.70 9S4.20: 14 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, R.290, Y.324 Ligands: 9SJ.21 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142 Hydrogen bonds: C:R.71, C:R.144, C:E.197, C:R.212, C:R.212 Water bridges: C:R.37, C:E.147, C:E.147, C:E.147, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.290 Halogen bonds: C:D.70 9S4.27: 14 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, R.290, Y.324 Ligands: 9SJ.28 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142 Hydrogen bonds: D:R.71, D:R.144, D:E.197, D:R.212, D:R.212 Water bridges: D:R.37, D:E.147, D:E.147, D:E.147, D:E.197 Salt bridges: D:R.37, D:R.212, D:R.290 Halogen bonds: D:D.70

4 x 9SJ: 5-acetamido-2,6-anhydro-3,5,7-trideoxy-3-fluoro-D-threo-L-galacto-nononic acid(Post Translational Modification)

9SJ.7: 15 residues within 4Å: Chain A: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 Ligands: 9S4.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.98, A:I.142, A:R.144 Hydrogen bonds: A:R.71, A:R.144, A:E.197, A:R.212, A:R.212 Water bridges: A:R.75, A:R.144, A:E.147, A:E.147, A:E.197 Salt bridges: A:R.37, A:R.212, A:R.290 Halogen bonds: A:D.70 9SJ.14: 15 residues within 4Å: Chain B: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 Ligands: 9S4.13 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.98, B:I.142, B:R.144 Hydrogen bonds: B:R.71, B:R.144, B:E.197, B:R.212, B:R.212 Water bridges: B:R.75, B:R.144, B:E.147, B:E.147, B:E.197 Salt bridges: B:R.37, B:R.212, B:R.290 Halogen bonds: B:D.70 9SJ.21: 15 residues within 4Å: Chain C: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 Ligands: 9S4.20 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:W.98, C:I.142, C:R.144 Hydrogen bonds: C:R.71, C:R.144, C:E.197, C:R.212, C:R.212 Water bridges: C:R.75, C:R.144, C:E.147, C:E.147, C:E.197 Salt bridges: C:R.37, C:R.212, C:R.290 Halogen bonds: C:D.70 9SJ.28: 15 residues within 4Å: Chain D: R.37, E.38, D.70, R.71, W.98, I.142, R.144, A.166, E.196, E.197, R.212, N.214, R.290, Y.324 Ligands: 9S4.27 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:W.98, D:I.142, D:R.144 Hydrogen bonds: D:R.71, D:R.144, D:E.197, D:R.212, D:R.212 Water bridges: D:R.75, D:R.144, D:E.147, D:E.147, D:E.197 Salt bridges: D:R.37, D:R.212, D:R.290 Halogen bonds: D:D.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McKimm-Breschkin, J.L. et al., Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. J. Med. Chem. (2018)

Release Date

2018-02-21

Peptides

Neuraminidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Neuraminidase

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