SMTL ID : 5ea7.1

Crystal Structure of Inhibitor BMS-433771 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: F.137, L.138, G.139, P.353, Q.354 Ligands: 5NO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.137, A:G.139, A:P.353, A:Q.354 SO4.2: 3 residues within 4Å: Chain A: L.231, T.234 Chain B: Y.250 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.88, B:Y.250 SO4.3: 1 residues within 4Å: Chain A: Q.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.94 SO4.4: 2 residues within 4Å: Chain A: T.91 Chain B: S.255 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.254, B:S.255 SO4.5: 3 residues within 4Å: Chain A: N.262, K.271, S.275 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.275 SO4.8: 6 residues within 4Å: Chain B: F.137, L.138, G.139, P.353, Q.354 Ligands: 5NO.21 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.137, B:G.139, B:P.353, B:Q.354 SO4.9: 3 residues within 4Å: Chain B: L.231, T.234 Chain C: Y.250 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.88, C:Y.250 SO4.10: 1 residues within 4Å: Chain B: Q.94 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.94 SO4.11: 2 residues within 4Å: Chain B: T.91 Chain C: S.255 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.254, C:S.255 SO4.12: 3 residues within 4Å: Chain B: N.262, K.271, S.275 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.275 SO4.15: 6 residues within 4Å: Chain C: F.137, L.138, G.139, P.353, Q.354 Ligands: 5NO.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.139, C:P.353, C:Q.354 SO4.16: 3 residues within 4Å: Chain A: Y.250 Chain C: L.231, T.234 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.250, C:N.88 SO4.17: 1 residues within 4Å: Chain C: Q.94 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.94 SO4.18: 2 residues within 4Å: Chain A: S.255 Chain C: T.91 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.254, A:S.255 SO4.19: 3 residues within 4Å: Chain C: N.262, K.271, S.275 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.275

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

NHE.6: 6 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, 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.13: 6 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, 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.20: 6 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, 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

3 x 5NO: 1-cyclopropyl-3-[[1-(4-oxidanylbutyl)benzimidazol-2-yl]methyl]imidazo[4,5-c]pyridin-2-one(Non-covalent)

5NO.7: 12 residues within 4Å: Chain A: F.488 Chain B: F.140, F.488, D.489 Chain C: F.140, M.396, D.486, E.487, F.488 Ligands: 5NO.14, SO4.15, 5NO.21 12 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:F.140, B:F.140, B:D.489, C:F.140, C:F.488, C:F.488, C:F.488, C:F.488, A:F.488 pi-Stacking: C:F.140, A:F.488, A:F.488 5NO.14: 12 residues within 4Å: Chain A: F.140, M.396, D.486, E.487, F.488 Chain B: F.488 Chain C: F.140, F.488, D.489 Ligands: SO4.1, 5NO.7, 5NO.21 12 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:F.140, A:F.488, A:F.488, A:F.488, A:F.488, B:F.488, C:F.140, C:F.140, C:D.489 pi-Stacking: A:F.140, B:F.488, B:F.488 5NO.21: 12 residues within 4Å: Chain A: F.140, F.488, D.489 Chain B: F.140, M.396, D.486, E.487, F.488 Chain C: F.488 Ligands: 5NO.7, SO4.8, 5NO.14 12 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:F.140, B:F.488, B:F.488, B:F.488, B:F.488, A:F.140, A:F.140, A:D.489, C:F.488 pi-Stacking: B:F.140, C: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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