Table 3 Binding conformation analysis of active compounds from the plasma profile of Huang-Lian-Jie-Du-Tang in the ligand-binding pocket of H1N1 neuraminidase (PDB ID 3B7E).

From: Inhibition activity of a traditional Chinese herbal formula Huang-Lian-Jie-Du-Tang and its major components found in its plasma profile on neuraminidase-1

Ligands

H-bonding to amino acid residues (distance, Ã…)

Hydrophobic contacts to amino acid residues

Baicalein

Glu227 (3.1, 3.2 Å), Glu277 (2.7, 3.2 Å), Tyr406 (2.9 Å)

Ser179, Ile222, Asn221, Arg224, Gly244, Ser246

Baicalin

—

—

Berberine

Ser179 (3.3 Å), Asn294 (3 Å)

Arg152, Trp178, Ser179, Ile222, Arg224, Glu227, Glu276, Glu277, Ser246, Arg292, Asn294, Asn347

Coptisine

Ser246 (2.9 Å)

Glu119, Asp151, Arg152, Trp178, Ile222, Glu227, Asn294, Asn347

Epiberberine

Ser246 (2.9 Å)

Glu119, Asp151, Arg152, Ser179, Trp178, Ile222, Arg224, Glu227, Glu277, Asn294, Asn347, Tyr406

Geniposide

Asp151 (1.6 Å), Trp178 (1.9, 2.0 Å), Glu227 (2.0 Å), Ser246 (3.1 Å), Arg292 (1.9, 3.0 Å), Asn294 (1.7 Å), Arg371 (1.9 Å), Tyr406 (3.1 Å)

Glu119, Ser179, Ile222, Arg224

Jatrorrhizine

—

Asp151, Arg152, Trp178, Asn221, Ile222, Arg224, Glu227, Ser246, Tyr406,

Oroxylin A

Arg118 (3.9 Å), Arg371 (3.9 Å)

Arg152, Asp151, Arg224, Glu227, Glu277, Arg292, Tyr406

Oroxylin A 7-O-β-D-glucuronide

Asn221 (2.9, 3.0 Å), Gly244 (3.1 Å), Ser246 (3.2 Å), Asn294 (2.3 Å)

Arg152, Trp178, Ser179, Ile222, Arg224, Glu227, Pro245, Arg292

Palmatine

—

Arg118, Glu119, Asp151, Trp178, Arg224, Glu277, Arg292, Asn294, Asn347, Arg371, Tyr406

Phellodendrine

Glu227 (3.2 Å)

Asp151, Trp178, Ser179, Arg224, Glu277, Arg292, Arg371, Tyr406

Wogonin

Ser246 (4.0 Å), Arg292 (3.2, 3.2, 3.8 Å), Tyr406 (3.3 Å)

Arg152, Trp178, Ser179, Ile222, Arg224, Glu227, Glu277

Wogonoside

Asp151 (1.7 Å), Arg156 (1.6 Å), Trp178 (2.8, 3.2 Å), Glu227 (1.7 Å), Glu277 (3.1 Å), Asn294 (2.0 Å)

Arg118, Glu119, Leu134, Ser179, Ile222, Arg224, Ser246, Arg292, Arg371, Tyr406

Sialic acid

Arg118 (1.7 Å), Glu119 (1.7 Å), Asp151 (1.7, 2.7 Å), Trp178 (3.2 Å), Glu227 (1.9, 3.1 Å), Glu277 (1.9 Å), Arg292 (1.7, 3.2 Å), Arg371 (1.8, 3.1 Å), Tyr406 (1.8 Å)

Ile222, Arg224

Zanamivir*

Arg118 (2.0 Å), Asp151 (1.7, 2.0 Å), Arg152 (1.7 Å), Trp178 (1.5, 3.1 Å), Glu227 (3.1 Å), Glu276 (1.6, 1.6 Å), Arg292 (3.1, 3.2 Å), Arg371 (3.0, 3.1 Å)

Glu119, Arg224, Ser246, Glu277, Asn294, Tyr406

  1. *neuraminidase inhibitor, positive control in the crystal structure; −: not observed.
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