SMTL ID : 5ea6.1

Crystal Structure of Inhibitor BTA-9881 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format

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.7: 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.13: 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

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

SO4.2: 4 residues within 4Å: Chain A: S.443, K.445, G.464, S.466 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.443, A:S.443, A:S.466 SO4.3: 4 residues within 4Å: Chain A: R.235, E.236, V.239, N.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.240 Salt bridges: A:R.235 SO4.4: 3 residues within 4Å: Chain A: N.276, N.277, R.364 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.276, A:N.277 Salt bridges: A:R.364 Water bridges: C:Q.98 SO4.5: 5 residues within 4Å: Chain A: N.444, K.445, G.446, D.448, K.461 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.444, A:G.446 Salt bridges: A:K.461 SO4.8: 4 residues within 4Å: Chain B: S.443, K.445, G.464, S.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.443, B:S.443, B:S.466 SO4.9: 4 residues within 4Å: Chain B: R.235, E.236, V.239, N.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.240 Salt bridges: B:R.235 SO4.10: 3 residues within 4Å: Chain B: N.276, N.277, R.364 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:Q.98 Hydrogen bonds: B:N.276, B:N.277 Salt bridges: B:R.364 SO4.11: 5 residues within 4Å: Chain B: N.444, K.445, G.446, D.448, K.461 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.444, B:G.446 Salt bridges: B:K.461 SO4.14: 4 residues within 4Å: Chain C: S.443, K.445, G.464, S.466 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.443, C:S.443, C:S.466 SO4.15: 4 residues within 4Å: Chain C: R.235, E.236, V.239, N.240 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.240 Salt bridges: C:R.235 SO4.16: 3 residues within 4Å: Chain C: N.276, N.277, R.364 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.276, C:N.277 Salt bridges: C:R.364 Water bridges: B:Q.98 SO4.17: 5 residues within 4Å: Chain C: N.444, K.445, G.446, D.448, K.461 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.444, C:G.446 Salt bridges: C:K.461

3 x 5NP: (9~{b}~{R})-9~{b}-(4-chlorophenyl)-1-pyridin-3-ylcarbonyl-2,3-dihydroimidazo[5,6]pyrrolo[1,2-~{a}]pyridin-5-one(Non-covalent)

5NP.6: 11 residues within 4Å: Chain A: F.137, F.140, M.396, F.488 Chain B: F.140, F.488 Chain C: F.140, M.396, F.488 Ligands: 5NP.12, 5NP.18 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:F.140, B:F.488 pi-Stacking: C:F.488, A:F.488, B:F.488 5NP.12: 11 residues within 4Å: Chain A: F.140, M.396, F.488 Chain B: F.137, F.140, M.396, F.488 Chain C: F.140, F.488 Ligands: 5NP.6, 5NP.18 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.140, C:F.488 pi-Stacking: A:F.488, C:F.488, B:F.488 5NP.18: 11 residues within 4Å: Chain A: F.140, F.488 Chain B: F.140, M.396, F.488 Chain C: F.137, F.140, M.396, F.488 Ligands: 5NP.6, 5NP.12 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A pi-Stacking: C:F.488, B:F.488, A:F.488 Hydrophobic interactions: B:F.140, A: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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