SMTL ID : 5ea5.1

Crystal Structure of Inhibitor TMC-353121 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.387, A:F.477, A:Y.478 Hydrogen bonds: A:D.479 NHE.5: 8 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477, B:Y.478 Hydrogen bonds: B:D.479 NHE.9: 8 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477, C:Y.478 Hydrogen bonds: C:D.479

3 x TM3: 2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol(Non-covalent)

TM3.2: 19 residues within 4Å: Chain A: F.140, D.486, E.487, F.488, K.498 Chain B: F.137, F.140, D.486, E.487, F.488, K.498 Chain C: F.140, D.486, E.487, F.488, D.489 Ligands: TM3.6, TAR.8, TM3.10 20 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: B:F.488, C:F.140, C:F.140, C:F.488, C:F.488, C:D.489, A:F.488, A:F.488 Hydrogen bonds: B:K.498, C:F.488, A:D.486, A:D.486, A:K.498 pi-Stacking: B:F.140, B:F.488, B:F.488, A:F.140 Salt bridges: C:E.487, A:D.486, A:E.487 TM3.6: 19 residues within 4Å: Chain A: F.140, D.486, E.487, F.488, D.489 Chain B: F.140, D.486, E.487, F.488, K.498 Chain C: F.137, F.140, D.486, E.487, F.488, K.498 Ligands: TM3.2, TM3.10, TAR.12 20 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: B:F.488, B:F.488, C:F.488, A:F.140, A:F.140, A:F.488, A:F.488, A:D.489 Hydrogen bonds: B:D.486, B:D.486, B:K.498, C:K.498, A:F.488 Salt bridges: B:D.486, B:E.487, A:E.487 pi-Stacking: B:F.140, C:F.140, C:F.488, C:F.488 TM3.10: 19 residues within 4Å: Chain A: F.137, F.140, D.486, E.487, F.488, K.498 Chain B: F.140, D.486, E.487, F.488, D.489 Chain C: F.140, D.486, E.487, F.488, K.498 Ligands: TM3.2, TAR.4, TM3.6 20 PLIP interactions: 7 interactions with chain B, 8 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: B:F.140, B:F.140, B:F.488, B:F.488, B:D.489, C:F.488, C:F.488, A:F.488 Hydrogen bonds: B:F.488, C:D.486, C:D.486, C:K.498, A:K.498 Salt bridges: B:E.487, C:D.486, C:E.487 pi-Stacking: C:F.140, A:F.140, A:F.488, A:F.488

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

SO4.3: 3 residues within 4Å: Chain A: N.276, N.277, R.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.276, A:N.277 Salt bridges: A:R.364 SO4.7: 3 residues within 4Å: Chain B: N.276, N.277, R.364 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.276, B:N.277 Salt bridges: B:R.364 SO4.11: 3 residues within 4Å: Chain C: N.276, N.277, R.364 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.276, C:N.277 Salt bridges: C:R.364

3 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.4: 6 residues within 4Å: Chain A: F.137, G.139, F.140, Q.354, E.356 Ligands: TM3.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.137, A:F.137, A:G.139, A:F.140, A:Q.354 TAR.8: 6 residues within 4Å: Chain B: F.137, G.139, F.140, Q.354, E.356 Ligands: TM3.2 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.137, B:F.137, B:G.139, B:F.140, B:Q.354 TAR.12: 6 residues within 4Å: Chain C: F.137, G.139, F.140, Q.354, E.356 Ligands: TM3.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.137, C:G.139, C:F.140, C:Q.354

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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