SMTL ID : 5kww.1

Crystal Structure of Inhibitor JNJ-53718678 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 NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: E.497, N.500 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.497 Water bridges: A:N.500 NAG.14: 2 residues within 4Å: Chain B: E.497, N.500 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.497 Water bridges: B:N.500 NAG.27: 2 residues within 4Å: Chain C: E.497, N.500 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.497 Water bridges: C:N.500

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

NHE.2: 7 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, V.482, N.496, I.499 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.387, A:F.477 Hydrogen bonds: A:F.477, A:F.477, A:D.479 Water bridges: A:D.479 NHE.15: 7 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, V.482, N.496, I.499 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477 Hydrogen bonds: B:F.477, B:F.477, B:D.479 NHE.28: 7 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, V.482, N.496, I.499 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477 Hydrogen bonds: C:F.477, C:F.477, C:D.479 Water bridges: C:D.479

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

SO4.3: 4 residues within 4Å: Chain C: R.235, E.236, V.239, N.240 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: C.358, K.359, V.360 Ligand excluded by PLIP SO4.5: 6 residues within 4Å: Chain A: F.137, L.138, G.139, Q.354 Ligands: 6YA.26, 6YA.39 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: E.328, G.418, K.419 Chain C: P.376 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: S.443, K.445, G.464, S.466 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: N.276, N.277, R.364 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: N.444, G.446, K.461 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: N.325, T.326, K.327 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: K.85 Chain B: Q.224 Ligand excluded by PLIP SO4.12: 8 residues within 4Å: Chain A: R.49, W.52, S.146, A.147, M.370 Chain B: L.456, Y.457, Y.458 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: R.235, E.236, V.239, N.240 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: C.358, K.359, V.360 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain B: F.137, L.138, G.139, Q.354 Ligands: 6YA.13, 6YA.39 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: P.376 Chain B: E.328, G.418, K.419 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain B: S.443, K.445, G.464, S.466 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain B: N.276, N.277, R.364 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: N.444, G.446, K.461 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain B: N.325, T.326, K.327 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain B: K.85 Chain C: Q.224 Ligand excluded by PLIP SO4.25: 8 residues within 4Å: Chain B: R.49, W.52, S.146, A.147, M.370 Chain C: L.456, Y.457, Y.458 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: R.235, E.236, V.239, N.240 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain C: C.358, K.359, V.360 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain C: F.137, L.138, G.139, Q.354 Ligands: 6YA.13, 6YA.26 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain B: P.376 Chain C: E.328, G.418, K.419 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain C: S.443, K.445, G.464, S.466 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain C: N.276, N.277, R.364 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain C: N.444, G.446, K.461 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain C: N.325, T.326, K.327 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain A: Q.224 Chain C: K.85 Ligand excluded by PLIP SO4.38: 8 residues within 4Å: Chain A: L.456, Y.457, Y.458 Chain C: R.49, W.52, S.146, A.147, M.370 Ligand excluded by PLIP

3 x 6YA: 3-[[5-chloranyl-1-(3-methylsulfonylpropyl)indol-2-yl]methyl]-1-[2,2,2-tris(fluoranyl)ethyl]imidazo[4,5-c]pyridin-2-one(Non-covalent)

6YA.13: 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: SO4.18, 6YA.26, SO4.31, 6YA.39 12 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:F.488, B:F.488, B:F.488, B:F.488, A:F.140, A:F.488, A:D.489 pi-Stacking: B:F.140, A:F.488, C:F.488, C:F.488 Halogen bonds: B:T.397 6YA.26: 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: SO4.5, 6YA.13, SO4.31, 6YA.39 12 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: B:F.140, B:F.488, B:D.489, C:F.488, C:F.488, C:F.488, C:F.488 pi-Stacking: B:F.488, A:F.488, A:F.488, C:F.140 Halogen bonds: C:T.397 6YA.39: 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: SO4.5, 6YA.13, SO4.18, 6YA.26 12 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A, 4 interactions with chain C pi-Stacking: B:F.488, B:F.488, A:F.140, C:F.488 Hydrophobic interactions: A:F.488, A:F.488, A:F.488, A:F.488, C:F.140, C:F.488, C:D.489 Halogen bonds: A:T.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roymans, D. et al., Therapeutic efficacy of a respiratory syncytial virus fusion inhibitor. Nat Commun (2017)

Release Date

2017-08-02

Peptides

Fusion glycoprotein F0, Envelope glycoprotein chimera: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0, Envelope glycoprotein chimera

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