SMTL ID : 6vkc.1

Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 8 residues within 4Å: Chain A: F.477, Y.478, D.479, V.482, N.496, I.499, N.500, L.503 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.478, A:V.482, A:I.499 Hydrogen bonds: A:D.479 NAG-FUC.11: 8 residues within 4Å: Chain B: F.477, Y.478, D.479, V.482, N.496, I.499, N.500, L.503 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.478, B:V.482, B:I.499 Hydrogen bonds: B:D.479 NAG-FUC.21: 8 residues within 4Å: Chain C: F.477, Y.478, D.479, V.482, N.496, I.499, N.500, L.503 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.478, C:V.482, C:I.499 Hydrogen bonds: C:D.479

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.12: 3 residues within 4Å: Chain A: W.52, S.146 Chain B: Y.458 Ligand excluded by PLIP CL.22: 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: 5 residues within 4Å: Chain A: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: G.471, E.472 Ligand excluded by PLIP SO4.8: 5 residues within 4Å: Chain A: K.498 Chain B: K.498 Chain C: K.498 Ligands: SO4.18, SO4.28 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: 4 residues within 4Å: Chain B: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: G.471, E.472 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain A: K.498 Chain B: K.498 Chain C: K.498 Ligands: SO4.8, SO4.28 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain C: S.443, K.445, G.464, K.465, S.466 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain C: V.192, L.193, D.194, K.226 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: L.273, N.276, N.277, R.364 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain C: N.444, K.445, G.446, K.461 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: G.471, E.472 Ligand excluded by PLIP SO4.28: 5 residues within 4Å: Chain A: K.498 Chain B: K.498 Chain C: K.498 Ligands: SO4.8, SO4.18 Ligand excluded by PLIP

3 x R0J: 3-{[5-chloro-1-(4,4,4-trifluorobutyl)-1H-imidazo[4,5-b]pyridin-2-yl]methyl}-1-cyclopropyl-1,3-dihydro-2H-imidazo[4,5-c]pyridin-2-one(Non-covalent)

R0J.9: 16 residues within 4Å: Chain A: F.137, F.140, M.396, T.397, D.486, E.487, F.488 Chain B: F.137, F.488 Chain C: F.140, F.488, D.489 Ligands: TAR.10, R0J.19, TAR.20, R0J.29 13 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: B:F.137, B:F.488, A:F.140, A:F.488, A:F.488, A:F.488, C:F.140, C:F.140, C:D.489 pi-Stacking: B:F.488, B:F.488, A:F.140, C:F.488 R0J.19: 16 residues within 4Å: Chain A: F.140, F.488, D.489 Chain B: F.137, F.140, M.396, T.397, D.486, E.487, F.488 Chain C: F.137, F.488 Ligands: R0J.9, TAR.20, R0J.29, TAR.30 13 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: B:F.140, B:F.488, B:F.488, B:F.488, A:F.140, A:F.140, A:D.489, C:F.137, C:F.488 pi-Stacking: B:F.140, A:F.488, C:F.488, C:F.488 R0J.29: 16 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, T.397, D.486, E.487, F.488 Ligands: R0J.9, TAR.10, R0J.19, TAR.30 13 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C, 4 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, A:F.137, A:F.488 pi-Stacking: B:F.488, C:F.140, A:F.488, A:F.488

3 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.10: 9 residues within 4Å: Chain A: F.137, L.138, G.139, F.140, P.353, Q.354, E.356 Ligands: R0J.9, R0J.29 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.137, A:F.137, A:F.137, A:F.137, A:G.139, A:F.140, A:Q.354 TAR.20: 9 residues within 4Å: Chain B: F.137, L.138, G.139, F.140, P.353, Q.354, E.356 Ligands: R0J.9, R0J.19 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.137, B:F.137, B:F.137, B:F.137, B:G.139, B:F.140, B:Q.354 TAR.30: 9 residues within 4Å: Chain C: F.137, L.138, G.139, F.140, P.353, Q.354, E.356 Ligands: R0J.19, R0J.29 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.137, C:F.137, C:F.137, C:G.139, C:F.140, 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),Envelope glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Prefusion RSV F (DS-Cav1),Envelope glycoprotein

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