SMTL ID : 6cfg.1

Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with small molecule JNJ4796

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.169, N.240, D.241, A.242 Chain E: S.221 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain B: E.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.147 NAG-NAG.7: 5 residues within 4Å: Chain A: S.221 Chain C: N.169, N.240, D.241, A.242 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: E.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.147 NAG-NAG.13: 5 residues within 4Å: Chain C: S.221 Chain E: N.169, N.240, D.241, A.242 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain F: E.147, E.150, S.151, N.154, T.156 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:E.147

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

NAG.3: 1 residues within 4Å: Chain A: N.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.27 NAG.4: 1 residues within 4Å: Chain A: N.290 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain C: N.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.27 NAG.10: 1 residues within 4Å: Chain C: N.290 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain E: N.27 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.27 NAG.16: 1 residues within 4Å: Chain E: N.290 No protein-ligand interaction detected (PLIP)

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)

EZ7.5: 17 residues within 4Å: Chain A: H.12, H.32, Q.34, S.292, T.319 Chain B: V.18, D.19, G.20, W.21, T.41, I.45, V.48, T.49, V.52, N.53, I.56 Ligands: PEG.6 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.21, B:V.48, B:V.52, B:I.56 Water bridges: B:N.53, A:A.33 Hydrogen bonds: A:T.319 pi-Stacking: A:H.12 EZ7.11: 17 residues within 4Å: Chain C: H.12, H.32, Q.34, S.292, T.319 Chain D: V.18, D.19, G.20, W.21, T.41, I.45, V.48, T.49, V.52, N.53, I.56 Ligands: PEG.12 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:T.319 Water bridges: C:A.33, D:N.53 pi-Stacking: C:H.12 Hydrophobic interactions: D:W.21, D:V.48, D:V.52, D:I.56 EZ7.17: 17 residues within 4Å: Chain E: H.12, H.32, Q.34, S.292, T.319 Chain F: V.18, D.19, G.20, W.21, T.41, I.45, V.48, T.49, V.52, N.53, I.56 Ligands: PEG.18 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:W.21, F:V.48, F:V.52, F:I.56 Water bridges: F:N.53, E:A.33 Hydrogen bonds: E:T.319 pi-Stacking: E:H.12

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 3 residues within 4Å: Chain B: T.49, N.53 Ligands: EZ7.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.53, B:N.53 PEG.12: 3 residues within 4Å: Chain D: T.49, N.53 Ligands: EZ7.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.53, D:N.53 PEG.18: 3 residues within 4Å: Chain F: T.49, N.53 Ligands: EZ7.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.53, F:N.53

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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