SMTL ID : 6vke.1

Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.387, A:F.387, A:F.477 Hydrogen bonds: A:D.479 Water bridges: A:D.479, A:D.479 NHE.9: 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.387, B:F.477 Hydrogen bonds: B:D.479 NHE.17: 8 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499, L.503 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.387, C:F.387, C:F.477 Hydrogen bonds: C:D.479 Water bridges: C:D.479, C:D.479

3 x R0S: 4-(5-chloro-2-{[1-(3,4-dimethoxyphenyl)-2-oxo-1,2-dihydro-3H-imidazo[4,5-c]pyridin-3-yl]methyl}-1H-indol-1-yl)butanenitrile(Non-covalent)

R0S.2: 14 residues within 4Å: Chain A: F.140, T.397, S.398, D.486, F.488 Chain B: F.137, F.488 Chain C: F.140, F.488, D.489 Ligands: SO4.8, R0S.10, SO4.16, R0S.18 15 PLIP interactions: 4 interactions with chain C, 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:F.140, C:F.140, C:F.488, C:D.489, A:F.140, A:F.140, A:F.488, A:F.488, A:F.488, A:F.488, B:F.488 pi-Stacking: A:F.140, B:F.488, B:F.488 Halogen bonds: A:T.397 R0S.10: 14 residues within 4Å: Chain A: F.140, F.488, D.489 Chain B: F.140, T.397, S.398, D.486, F.488 Chain C: F.137, F.488 Ligands: R0S.2, SO4.16, R0S.18, SO4.24 15 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:F.140, B:F.140, B:F.488, B:F.488, B:F.488, B:F.488, A:F.140, A:F.140, A:F.488, A:D.489, C:F.488 pi-Stacking: B:F.140, C:F.488, C:F.488 Halogen bonds: B:T.397 R0S.18: 14 residues within 4Å: Chain A: F.137, F.488 Chain B: F.140, F.488, D.489 Chain C: F.140, T.397, S.398, D.486, F.488 Ligands: R0S.2, SO4.8, R0S.10, SO4.24 15 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: B:F.140, B:F.140, B:F.488, B:D.489, A:F.488, C:F.140, C:F.140, C:F.488, C:F.488, C:F.488, C:F.488 pi-Stacking: A:F.488, A:F.488, C:F.140 Halogen bonds: C:T.397

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: K.315, W.341 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: N.460, Q.462 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: K.315, W.341 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: N.460, Q.462 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: K.315, W.341 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: N.460, Q.462 Ligand excluded by PLIP

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

SO4.5: 4 residues within 4Å: Chain A: L.273, 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 SO4.6: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.443, A:S.466, A:S.466 Water bridges: A:G.464 Salt bridges: A:K.445 SO4.7: 4 residues within 4Å: Chain A: N.444, K.445, G.446, 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: 6 residues within 4Å: Chain A: F.137, L.138, G.139, Q.354 Ligands: R0S.2, R0S.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.137, A:F.137, A:G.139, A:Q.354 SO4.13: 4 residues within 4Å: Chain B: L.273, 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 SO4.14: 5 residues within 4Å: Chain B: S.443, K.445, G.464, K.465, S.466 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.443, B:S.466, B:S.466 Water bridges: B:G.464 Salt bridges: B:K.445 SO4.15: 4 residues within 4Å: Chain B: N.444, K.445, G.446, K.461 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.444, B:G.446 Salt bridges: B:K.461 SO4.16: 6 residues within 4Å: Chain B: F.137, L.138, G.139, Q.354 Ligands: R0S.2, R0S.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.137, B:F.137, B:G.139, B:Q.354 SO4.21: 4 residues within 4Å: Chain C: L.273, 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 SO4.22: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.443, C:S.466, C:S.466 Water bridges: C:G.464 Salt bridges: C:K.445 SO4.23: 4 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.444, C:G.446 Salt bridges: C:K.461 SO4.24: 6 residues within 4Å: Chain C: F.137, L.138, G.139, Q.354 Ligands: R0S.10, R0S.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.137, C:G.139, C:Q.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vendeville, S. et al., Discovery of 3-({5-Chloro-1-[3-(methylsulfonyl)propyl]-1H-indol-2-yl}methyl)-1-(2,2,2-trifluoroethyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one (JNJ-53718678), a Potent and Orally Bioavailable Fusion Inhibitor of Respiratory Syncytial Virus. J.Med.Chem. (2020)

Release Date

2020-05-27

Peptides

Prefusion RSV F (DS-Cav1): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Prefusion RSV F (DS-Cav1)

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