SMTL ID : 5ea4.1

Crystal Structure of Inhibitor JNJ-49153390 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

NHE.1: 8 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.387, A:F.477 Hydrogen bonds: A:D.479 NHE.8: 8 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477 Hydrogen bonds: B:D.479 NHE.15: 8 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477 Hydrogen bonds: C:D.479

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

SO4.2: 4 residues within 4Å: Chain A: L.273, N.276, N.277, R.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.276, A:N.277 Water bridges: A:R.364 Salt bridges: A:R.364 SO4.3: 3 residues within 4Å: Chain A: L.193, D.194, K.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.192, A:D.194 Salt bridges: A:K.226 SO4.4: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.443, A:S.466 Water bridges: A:S.443, A:G.464 SO4.5: 5 residues within 4Å: Chain A: N.444, K.445, G.446, V.447, K.461 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.446, A:V.447 Salt bridges: A:K.461 SO4.6: 5 residues within 4Å: Chain A: F.137, L.138, G.139, Q.354 Ligands: 5NM.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.137, A:G.139, A:Q.354 Water bridges: A:F.140, A:F.140 SO4.9: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.276, B:N.277 Water bridges: B:R.364 Salt bridges: B:R.364 SO4.10: 3 residues within 4Å: Chain B: L.193, D.194, K.226 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.192, B:D.194 Salt bridges: B:K.226 SO4.11: 5 residues within 4Å: Chain B: S.443, K.445, G.464, K.465, S.466 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.443, B:S.466 Water bridges: B:S.443, B:G.464 SO4.12: 5 residues within 4Å: Chain B: N.444, K.445, G.446, V.447, K.461 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.446, B:V.447 Salt bridges: B:K.461 SO4.13: 5 residues within 4Å: Chain B: F.137, L.138, G.139, Q.354 Ligands: 5NM.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.137, B:G.139, B:Q.354 Water bridges: B:F.140, B:F.140 SO4.16: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.276, C:N.277 Water bridges: C:R.364 Salt bridges: C:R.364 SO4.17: 3 residues within 4Å: Chain C: L.193, D.194, K.226 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.192, C:D.194 Salt bridges: C:K.226 SO4.18: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.443, C:S.466 Water bridges: C:S.443, C:G.464 SO4.19: 5 residues within 4Å: Chain C: N.444, K.445, G.446, V.447, K.461 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.446, C:V.447 Salt bridges: C:K.461 SO4.20: 5 residues within 4Å: Chain C: F.137, L.138, G.139, Q.354 Ligands: 5NM.21 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.139, C:Q.354 Water bridges: C:F.140, C:F.140

3 x 5NM: 3-[[5-bromanyl-1-(3-methylsulfonylpropyl)benzimidazol-2-yl]methyl]-1-cyclopropyl-imidazo[4,5-c]pyridin-2-one(Non-covalent)

5NM.7: 15 residues within 4Å: Chain A: F.137, F.140, M.396, T.397, S.398, D.486, F.488, D.489 Chain B: F.488 Chain C: F.140, F.488, D.489 Ligands: SO4.6, 5NM.14, 5NM.21 10 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:F.488, B:F.488, A:F.488, A:F.488, A:F.488, C:F.140 pi-Stacking: B:F.488, A:F.140, C:F.488 Halogen bonds: A:T.397 5NM.14: 15 residues within 4Å: Chain A: F.140, F.488, D.489 Chain B: F.137, F.140, M.396, T.397, S.398, D.486, F.488, D.489 Chain C: F.488 Ligands: 5NM.7, SO4.13, 5NM.21 10 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:F.488, B:F.488, B:F.488, A:F.140, C:F.488, C:F.488 pi-Stacking: B:F.140, A:F.488, C:F.488 Halogen bonds: B:T.397 5NM.21: 15 residues within 4Å: Chain A: F.488 Chain B: F.140, F.488, D.489 Chain C: F.137, F.140, M.396, T.397, S.398, D.486, F.488, D.489 Ligands: 5NM.7, 5NM.14, SO4.20 10 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:F.140, C:F.488, C:F.488, C:F.488, A:F.488, A:F.488 pi-Stacking: B:F.488, C:F.140, A:F.488 Halogen bonds: C:T.397

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

Related Entries With Identical Sequence