SMTL ID : 3qgh.1

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-cyclopropyl-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 2.14 Å

Oligo State

monomer

Ligands

1 x 63F: N-cyclopropyl-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide(Non-covalent)

63F.1: 27 residues within 4Å: Chain A: V.180, P.184, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.184, A:Y.192, A:F.194, A:F.194, A:I.448, A:Y.449, A:Y.449, A:A.451, A:L.467 Hydrogen bonds: A:Y.192, A:Y.192, A:Y.196, A:S.289, A:S.369

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: E.238, A.239, Q.242, K.255 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.238, A:E.238, A:K.255, A:K.255 Salt bridges: A:K.255 PO4.3: 5 residues within 4Å: Chain A: R.49, K.52, T.222, R.223, C.224 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.222, A:C.224 Water bridges: A:K.52, A:K.52, A:F.225 Salt bridges: A:R.49, A:K.52 PO4.4: 4 residues within 4Å: Chain A: R.506, V.531, R.532, T.533 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.532, A:T.533, A:T.533 Salt bridges: A:R.506 PO4.5: 8 residues within 4Å: Chain A: Q.20, Y.39, S.40, T.41, T.42, R.44, S.45, R.155 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.20, A:Q.20, A:T.41, A:T.42, A:T.42, A:S.45 Water bridges: A:S.45, A:S.45 Salt bridges: A:R.155 PO4.6: 4 residues within 4Å: Chain A: R.49, V.53, R.159, L.160 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.160, A:L.160 Salt bridges: A:R.49

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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