SMTL ID : 5ea3.1

Crystal Structure of Inhibitor JNJ-2408068 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

3 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.1: 7 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.387, A:F.387, A:F.477 Hydrogen bonds: A:D.479 NHE.9: 7 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.387, B:F.387, B:F.477 Hydrogen bonds: B:D.479 NHE.17: 7 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.387, C:F.477 Hydrogen bonds: C:D.479

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: N.276, N.277, R.364 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: F.137, R.339 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: S.443, K.445, S.466 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: E.236, V.239, N.240 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: Q.462, E.463 Chain C: K.156 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: N.276, N.277, R.364 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: F.137, R.339 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: S.443, K.445, S.466 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: E.236, V.239, N.240 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: K.156 Chain B: Q.462, E.463 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: N.276, N.277, R.364 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain C: F.137, R.339 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain C: S.443, K.445, S.466 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: E.236, V.239, N.240 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: K.156 Chain C: Q.462, E.463 Ligand excluded by PLIP

3 x 5NK: 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol(Non-covalent)

5NK.8: 13 residues within 4Å: Chain A: F.140, D.486, E.487, F.488, D.489 Chain B: M.396, D.486, F.488 Chain C: F.140, D.486, F.488 Ligands: 5NK.16, 5NK.24 18 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: B:F.488, A:F.140, A:F.488, A:F.488, A:F.488, A:D.489, C:F.140, C:F.140, C:F.488, C:F.488 Hydrogen bonds: B:D.486, B:D.486 Salt bridges: B:D.486, A:D.486, A:E.487, C:D.486 pi-Stacking: B:F.488, A:F.488 5NK.16: 13 residues within 4Å: Chain A: F.140, D.486, F.488 Chain B: F.140, D.486, E.487, F.488, D.489 Chain C: M.396, D.486, F.488 Ligands: 5NK.8, 5NK.24 18 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: B:F.140, B:F.488, B:F.488, B:F.488, B:D.489, A:F.140, A:F.140, A:F.488, A:F.488, C:F.488 Salt bridges: B:D.486, B:E.487, A:D.486, C:D.486 pi-Stacking: B:F.488, C:F.488 Hydrogen bonds: C:D.486, C:D.486 5NK.24: 13 residues within 4Å: Chain A: M.396, D.486, F.488 Chain B: F.140, D.486, F.488 Chain C: F.140, D.486, E.487, F.488, D.489 Ligands: 5NK.8, 5NK.16 17 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: B:F.140, B:F.140, B:F.488, B:F.488, A:F.488, C:F.140, C:F.488, C:F.488, C:F.488, C:D.489 Salt bridges: B:D.486, A:D.486, C:D.486, C:E.487 Hydrogen bonds: A:D.486 pi-Stacking: A:F.488, C:F.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Molecular mechanism of respiratory syncytial virus fusion inhibitors. Nat.Chem.Biol. (2016)

Release Date

2015-12-09

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0

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