SMTL ID : 3qgi.1

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-[(2S)-butan-2-yl]-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 33F: N-[(2S)-butan-2-yl]-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide(Non-covalent)

33F.1: 27 residues within 4Å: Chain A: V.180, Y.192, G.193, F.194, Y.196, S.197, P.198, R.201, S.289, C.290, C.367, S.369, L.385, I.414, M.415, F.416, I.448, Y.449, A.451, Y.453, I.455, I.463, L.467, L.548, F.552, Y.556 Ligands: GOL.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.192, A:F.194, A:F.194, A:I.448, A:Y.449, A:Y.449, A:A.451 Hydrogen bonds: A:Y.192, A:Y.192, A:Y.196, A:S.289, A:S.369 Water bridges: A:S.197 pi-Cation interactions: A:R.201

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: L.27, A.436, R.437 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.437, A:R.437 GOL.3: 4 residues within 4Å: Chain A: R.305, A.306, A.307, G.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.305, A:R.305 GOL.4: 5 residues within 4Å: Chain A: S.408, G.411, N.412, M.415, E.447 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.408, A:G.411, A:N.412, A:E.447 Water bridges: A:R.395 GOL.5: 8 residues within 4Å: Chain A: E.362, N.370, S.372, T.386, S.479, G.481, E.482, R.485 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.362, A:N.370, A:S.372, A:S.479, A:E.482, A:E.482 Water bridges: A:V.373 GOL.6: 2 residues within 4Å: Chain A: Y.277, R.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.279 GOL.7: 3 residues within 4Å: Chain A: D.245, L.246, R.251 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.246, A:R.251 Water bridges: A:R.251 GOL.8: 3 residues within 4Å: Chain A: E.238, Q.242, K.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.255, A:K.255 GOL.9: 8 residues within 4Å: Chain A: E.399, N.407, W.409, V.433, L.434, R.437, Q.439, L.444 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.409, A:R.437, A:R.437, A:Q.439 GOL.10: 5 residues within 4Å: Chain A: M.424, L.498, R.499, R.502 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.502, A:R.502 GOL.11: 5 residues within 4Å: Chain A: Y.525, T.538, P.539, I.540, A.541 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.525, A:T.538, A:T.538, A:A.541 Water bridges: A:K.524, A:A.542 GOL.12: 6 residues within 4Å: Chain A: L.92, Y.177, A.451, G.555, Y.556 Ligands: 33F.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.177, A:Y.177 Water bridges: A:C.452, A:C.452 GOL.13: 5 residues within 4Å: Chain A: S.40, N.143, E.144, V.145, W.398 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.40 Water bridges: A:E.19, A:E.19, A:E.19, A:V.145 GOL.14: 3 residues within 4Å: Chain A: N.484, A.487, R.491 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.484, A:R.491, A:R.491 GOL.15: 6 residues within 4Å: Chain A: L.475, H.476, Y.478, R.502, W.529 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.475, A:R.502, A:R.502 Water bridges: A:S.477

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gentles, R.G. et al., Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-04-20

Peptides

RNA-directed RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-directed RNA polymerase

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