SMTL ID : 6eak.1

CRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN ESCAPE VARIANT T400A STABILIZED IN THE PREFUSION STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: K.75, N.216, I.217, E.218 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: F.137, R.339, Q.354 Chain C: R.106 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: K.75, N.216, I.217, E.218 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: R.106 Chain B: F.137, R.339, Q.354 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: K.75, N.216, I.217, E.218 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: R.106 Chain C: F.137, R.339, Q.354 Ligand excluded by PLIP

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

NHE.7: 8 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.387, A:F.387, A:F.477 Hydrogen bonds: A:D.479, A:N.496 NHE.16: 8 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.387, B:F.387, B:F.477 Hydrogen bonds: B:D.479, B:N.496 NHE.25: 8 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.387, C:F.387, C:F.477 Hydrogen bonds: C:D.479, C:N.496

3 x NI: NICKEL (II) ION(Non-covalent)

NI.8: 3 residues within 4Å: Chain A: Y.458 Chain C: W.52, S.146 No protein-ligand interaction detected (PLIP) NI.17: 3 residues within 4Å: Chain A: W.52, S.146 Chain B: Y.458 No protein-ligand interaction detected (PLIP) NI.26: 3 residues within 4Å: Chain B: W.52, S.146 Chain C: Y.458 No protein-ligand interaction detected (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.9: 15 residues within 4Å: Chain A: F.140, D.486, F.488, D.489, K.498 Chain B: M.396, D.486, E.487, F.488, K.498 Chain C: F.140, D.486, F.488 Ligands: 5NK.18, 5NK.27 24 PLIP interactions: 11 interactions with chain A, 7 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: A:F.140, A:F.140, A:F.488, A:F.488, A:F.488, A:D.489, C:F.140, C:F.140, C:F.140, C:F.488, B:F.488, B:F.488 Hydrogen bonds: A:K.498, B:K.498, B:K.498 Salt bridges: A:D.486, A:E.487, C:D.486, C:E.487, B:D.486, B:E.487 pi-Stacking: A:F.488, A:F.488, C:F.488 5NK.18: 15 residues within 4Å: Chain A: F.140, D.486, F.488 Chain B: F.140, D.486, F.488, D.489, K.498 Chain C: M.396, D.486, E.487, F.488, K.498 Ligands: 5NK.9, 5NK.27 24 PLIP interactions: 7 interactions with chain A, 6 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: A:F.140, A:F.140, A:F.140, A:F.488, C:F.488, C:F.488, B:F.140, B:F.140, B:F.488, B:F.488, B:F.488, B:D.489 Salt bridges: A:D.486, A:E.487, C:D.486, C:E.487, B:D.486, B:E.487 pi-Stacking: A:F.488, B:F.488, B:F.488 Hydrogen bonds: C:K.498, C:K.498, B:K.498 5NK.27: 15 residues within 4Å: Chain A: M.396, D.486, E.487, F.488, K.498 Chain B: F.140, D.486, F.488 Chain C: F.140, D.486, F.488, D.489, K.498 Ligands: 5NK.9, 5NK.18 24 PLIP interactions: 6 interactions with chain A, 11 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: A:F.488, A:F.488, C:F.140, C:F.140, C:F.488, C:F.488, C:F.488, C:D.489, B:F.140, B:F.140, B:F.140, B:F.488 Hydrogen bonds: A:D.486, A:K.498, C:K.498 Salt bridges: A:D.486, A:E.487, C:D.486, C:E.487, B:D.486, B:E.487 pi-Stacking: C:F.488, C:F.488, B:F.488

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance. To be published

Release Date

2019-08-07

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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