SMTL ID : 3kpe.1

Solution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed with TMC353121, a small-moleucule inhibitor of RSV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

hetero-3-3-mer

Ligands

3 x TM3: 2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol(Non-covalent)

TM3.1: 14 residues within 4Å: Chain A: D.36, L.37, N.39, Y.40, K.43, Q.44 Chain B: S.4, D.5, E.6, F.7 Chain E: K.38, D.42, K.43 Ligands: PG4.2 15 PLIP interactions: 7 interactions with chain A, 3 interactions with chain E, 5 interactions with chain B Hydrophobic interactions: A:D.36, A:L.37, A:Y.40, A:Y.40, A:K.43, A:Q.44, E:K.38, B:F.7 pi-Stacking: A:Y.40 Water bridges: E:K.38 Salt bridges: E:D.42 Hydrogen bonds: B:D.5, B:D.5, B:D.5, B:E.6 TM3.3: 14 residues within 4Å: Chain A: K.38, D.42, K.43 Chain C: D.36, L.37, N.39, Y.40, K.43, Q.44 Chain D: S.4, D.5, E.6, F.7 Ligands: PG4.4 15 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: D:F.7, A:K.38, C:D.36, C:L.37, C:Y.40, C:Y.40, C:K.43, C:Q.44 Hydrogen bonds: D:D.5, D:D.5, D:D.5 Water bridges: A:K.38, A:D.42 Salt bridges: A:D.42 pi-Stacking: C:Y.40 TM3.5: 14 residues within 4Å: Chain C: K.38, D.42, K.43 Chain E: D.36, L.37, N.39, Y.40, K.43, Q.44 Chain F: S.4, D.5, E.6, F.7 Ligands: PG4.6 15 PLIP interactions: 7 interactions with chain E, 3 interactions with chain C, 5 interactions with chain F Hydrophobic interactions: E:D.36, E:L.37, E:Y.40, E:Y.40, E:K.43, E:Q.44, C:K.38, F:F.7 pi-Stacking: E:Y.40 Water bridges: C:K.38 Salt bridges: C:D.42 Hydrogen bonds: F:D.5, F:D.5, F:D.5, F:E.6

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: Y.40, Q.44, I.48 Chain E: D.42, L.46 Ligands: TM3.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.44 PG4.4: 6 residues within 4Å: Chain A: D.42, L.46 Chain C: Y.40, Q.44, I.48 Ligands: TM3.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.44 PG4.6: 6 residues within 4Å: Chain C: D.42, L.46 Chain E: Y.40, Q.44, I.48 Ligands: TM3.5 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roymans, D. et al., Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2009-12-22

Peptides

Fusion glycoprotein F0: ACE
Fusion glycoprotein F0: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Fusion glycoprotein F0

Fusion glycoprotein F0