SMTL ID : 8phi.1

Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 in complex with Lonafarnib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-trimer

Ligands

3 x 336: 4-{2-[4-(3,10-DIBROMO-8-CHLORO-6,11-DIHYDRO-5H-BENZO[5,6]CYCLOHEPTA[1,2-B]PYRIDIN-11-YL)PIPERIDIN-1-YL]-2-OXOETHYL}PIPERIDINE-1-CARBOXAMIDE(Non-covalent)

336.1: 13 residues within 4Å: Chain A: F.112, F.115, F.463 Chain B: F.115, M.371, F.463 Chain C: F.112, F.115, M.371, F.463, D.464 Ligands: 336.6, 336.11 14 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:F.115, B:F.115, B:F.463, B:F.463, A:F.112, A:F.112, A:F.463, A:F.463, A:F.463, A:F.463, C:F.115 pi-Stacking: B:F.463, C:F.463, C:F.463 336.6: 13 residues within 4Å: Chain A: F.112, F.115, M.371, F.463, D.464 Chain B: F.112, F.115, F.463 Chain C: F.115, M.371, F.463 Ligands: 336.1, 336.11 14 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: A:F.115, B:F.112, B:F.112, B:F.463, B:F.463, B:F.463, B:F.463, C:F.115, C:F.115, C:F.463, C:F.463 pi-Stacking: A:F.463, A:F.463, C:F.463 336.11: 13 residues within 4Å: Chain A: F.115, M.371, F.463 Chain B: F.112, F.115, M.371, F.463, D.464 Chain C: F.112, F.115, F.463 Ligands: 336.1, 336.6 14 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: A:F.115, A:F.115, A:F.463, A:F.463, B:F.115, C:F.112, C:F.112, C:F.463, C:F.463, C:F.463, C:F.463 pi-Stacking: A:F.463, B:F.463, B:F.463

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

SO4.2: 5 residues within 4Å: Chain A: E.35, L.147, K.166, D.169, N.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.35 Water bridges: A:L.147, A:K.166, A:N.172 Salt bridges: A:K.166 SO4.7: 5 residues within 4Å: Chain B: E.35, L.147, K.166, D.169, N.172 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.35 Water bridges: B:L.147, B:K.166, B:N.172 Salt bridges: B:K.166 SO4.12: 5 residues within 4Å: Chain C: E.35, L.147, K.166, D.169, N.172 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.35 Water bridges: C:L.147, C:K.166, C:N.172 Salt bridges: C:K.166

6 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PG0.4: 2 residues within 4Å: Chain A: E.447, N.451 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.451 PG0.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PG0.9: 2 residues within 4Å: Chain B: E.447, N.451 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.451 PG0.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PG0.14: 2 residues within 4Å: Chain C: E.447, N.451 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.451

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: Y.433 Chain B: W.27 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain B: Y.433 Chain C: W.27 No protein-ligand interaction detected (PLIP) CA.15: 2 residues within 4Å: Chain A: W.27 Chain C: Y.433 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sake, S.M. et al., Drug repurposing screen identifies lonafarnib as respiratory syncytial virus fusion protein inhibitor. Nat Commun (2024)

Release Date

2024-02-21

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0