SMTL ID : 6cf7.1

Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in complex with small molecule JNJ4796

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: 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.1: 1 residues within 4Å: Chain A: N.286 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 1 residues within 4Å: Chain C: N.286 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 1 residues within 4Å: Chain E: N.286 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 1 residues within 4Å: Chain A: N.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 1 residues within 4Å: Chain C: N.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 1 residues within 4Å: Chain E: N.11 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 6 residues within 4Å: Chain A: N.64, E.86, N.87, C.90, S.136, R.220 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.23 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: N.64, E.86, N.87, C.90, S.136, R.220 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.23 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain E: N.64, E.86, N.87, C.90, S.136, R.220 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain E: N.23 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.54 NAG.11: 1 residues within 4Å: Chain C: N.54 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.54 NAG.17: 1 residues within 4Å: Chain E: N.54 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.54

3 x EZ7: N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl)methyl]piperazine-1-carbonyl}pyridin-4-yl)-1,3-benzoxazol-5-yl]acetamide(Non-covalent)

EZ7.6: 17 residues within 4Å: Chain A: H.8, H.28, V.30, S.288, L.289, T.315 Chain B: V.18, D.19, G.20, W.21, T.41, I.45, I.48, T.49, V.52, N.53, I.56 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.48, B:V.52, A:L.289, A:T.315 Hydrogen bonds: A:T.315 pi-Stacking: A:H.8 EZ7.12: 17 residues within 4Å: Chain C: H.8, H.28, V.30, S.288, L.289, T.315 Chain D: V.18, D.19, G.20, W.21, T.41, I.45, I.48, T.49, V.52, N.53, I.56 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.289, C:T.315, D:I.48, D:V.52 pi-Stacking: C:H.8 EZ7.18: 17 residues within 4Å: Chain E: H.8, H.28, V.30, S.288, L.289, T.315 Chain F: V.18, D.19, G.20, W.21, T.41, I.45, I.48, T.49, V.52, N.53, I.56 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.289, E:T.315, F:I.48, F:V.52 Hydrogen bonds: E:T.315 pi-Stacking: E:H.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Dongen, M.J.P. et al., A small-molecule fusion inhibitor of influenza virus is orally active in mice. Science (2019)

Release Date

2019-02-13

Peptides

Hemagglutinin: ACE
Hemagglutinin: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Hemagglutinin

Hemagglutinin

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