SMTL ID : 6eag.1

CRYSTAL STRUCTURE OF FUSION INHIBITOR JNJ-2408068 IN COMPLEX WITH HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN ESCAPE VARIANT G143S STABILIZED IN THE PREFUSION STATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-trimer

Ligands

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

NHE.1: 6 residues within 4Å: Chain A: F.387, F.477, Y.478, D.479, N.496, I.499 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.387, A:F.477, A:Y.478 Hydrogen bonds: A:D.479 NHE.6: 6 residues within 4Å: Chain B: F.387, F.477, Y.478, D.479, N.496, I.499 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.387, B:F.477, B:Y.478 Hydrogen bonds: B:D.479 NHE.11: 6 residues within 4Å: Chain C: F.387, F.477, Y.478, D.479, N.496, I.499 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.477, C:Y.478 Hydrogen bonds: C:D.479

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

SO4.2: 4 residues within 4Å: Chain A: F.137, L.138, G.139, Q.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.137, A:F.137, A:G.139, A:Q.354 SO4.3: 3 residues within 4Å: Chain A: N.444, G.446, K.461 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.446 Salt bridges: A:K.461 SO4.7: 4 residues within 4Å: Chain B: F.137, L.138, G.139, Q.354 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.137, B:F.137, B:G.139, B:Q.354 SO4.8: 3 residues within 4Å: Chain B: N.444, G.446, K.461 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.446 Salt bridges: B:K.461 SO4.12: 4 residues within 4Å: Chain C: F.137, L.138, G.139, Q.354 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.137, C:G.139, C:Q.354 SO4.13: 3 residues within 4Å: Chain C: N.444, G.446, K.461 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.446 Salt bridges: C:K.461

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

TAR.4: 5 residues within 4Å: Chain A: K.315, W.341, A.355, C.358, V.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.355, A:V.360 Salt bridges: A:K.315 TAR.9: 5 residues within 4Å: Chain B: K.315, W.341, A.355, C.358, V.360 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.355, B:V.360 Salt bridges: B:K.315 TAR.14: 5 residues within 4Å: Chain C: K.315, W.341, A.355, C.358, V.360 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.355, C:V.360 Salt bridges: C:K.315

3 x 5NK: 2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol(Non-covalent)

5NK.5: 15 residues within 4Å: Chain A: F.140, M.396, D.486, F.488, D.489 Chain B: M.396, D.486, E.487, F.488 Chain C: F.140, D.486, F.488, D.489 Ligands: 5NK.10, 5NK.15 19 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: C:F.140, C:F.140, C:F.488, C:D.489, B:F.488, B:F.488, A:F.140, A:F.140, A:F.488, A:F.488, A:F.488, A:D.489 Salt bridges: C:D.486, B:D.486, A:D.486, A:E.487 Hydrogen bonds: B:E.487 pi-Stacking: B:F.488, A:F.488 5NK.10: 15 residues within 4Å: Chain A: F.140, D.486, F.488, D.489 Chain B: F.140, M.396, D.486, F.488, D.489 Chain C: M.396, D.486, E.487, F.488 Ligands: 5NK.5, 5NK.15 19 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: B:F.140, B:F.140, B:F.488, B:F.488, B:F.488, B:D.489, C:F.488, C:F.488, A:F.140, A:F.140, A:F.488, A:D.489 Salt bridges: B:D.486, B:E.487, C:D.486, A:D.486 pi-Stacking: B:F.488, C:F.488 Hydrogen bonds: C:E.487 5NK.15: 15 residues within 4Å: Chain A: M.396, D.486, E.487, F.488 Chain B: F.140, D.486, F.488, D.489 Chain C: F.140, M.396, D.486, F.488, D.489 Ligands: 5NK.5, 5NK.10 19 PLIP interactions: 9 interactions with chain C, 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: C:F.140, C:F.140, C:F.488, C:F.488, C:F.488, C:D.489, B:F.140, B:F.140, B:F.488, B:D.489, A:F.488, A:F.488 Salt bridges: C:D.486, C:E.487, B:D.486, A:D.486 pi-Stacking: C:F.488, A:F.488 Hydrogen bonds: B:D.486

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Battles, M.B. et al., Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance. To be published

Release Date

2019-08-07

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

Fusion glycoprotein F0

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