SMTL ID : 6vkd.1

Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x R0P: 1-cyclopropyl-3-({1-[3-(methylsulfonyl)propyl]-1H-pyrrolo[3,2-c]pyridin-2-yl}methyl)-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one(Non-covalent)

R0P.1: 13 residues within 4Å: Chain A: F.137, F.140, M.396, D.486, F.488 Chain B: F.137, F.488 Chain C: F.140, F.488, D.489 Ligands: SO4.6, R0P.9, R0P.17 11 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:F.140, A:F.488, A:F.488, B:F.137, B:F.488, C:F.140, C:F.488, C:F.488 pi-Stacking: A:F.140, B:F.488, B:F.488 R0P.9: 13 residues within 4Å: Chain A: F.140, F.488, D.489 Chain B: F.137, F.140, M.396, D.486, F.488 Chain C: F.137, F.488 Ligands: R0P.1, SO4.14, R0P.17 11 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: A:F.140, A:F.488, A:F.488, B:F.140, B:F.488, B:F.488, C:F.137, C:F.488 pi-Stacking: B:F.140, C:F.488, C:F.488 R0P.17: 13 residues within 4Å: Chain A: F.137, F.488 Chain B: F.140, F.488, D.489 Chain C: F.137, F.140, M.396, D.486, F.488 Ligands: R0P.1, R0P.9, SO4.22 11 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: A:F.137, A:F.488, B:F.140, B:F.488, B:F.488, C:F.140, C:F.488, C:F.488 pi-Stacking: A:F.488, A:F.488, C:F.140

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

CL.2: 3 residues within 4Å: Chain A: Y.458 Chain C: W.52, S.146 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: W.52, S.146 Chain B: Y.458 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: W.52, S.146 Chain C: Y.458 Ligand excluded by PLIP

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

SO4.3: 4 residues within 4Å: Chain A: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: K.427, N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: F.137, G.139, P.353, Q.354 Ligands: R0P.1 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: K.293, E.294 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: K.427, N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: F.137, G.139, P.353, Q.354 Ligands: R0P.9 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: K.293, E.294 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain C: K.427, N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: F.137, G.139, P.353, Q.354 Ligands: R0P.17 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: K.293, E.294 Ligand excluded by PLIP

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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