SMTL ID : 5qj0.1

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 6-[ethyl(methylsulfonyl)amino]-2-(4-fluorophenyl)-N-methyl-5-(3-{[1-(pyrimidin-2-yl)cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

1 x J6D: 6-[ethyl(methylsulfonyl)amino]-2-(4-fluorophenyl)-N-methyl-5-(3-{[1-(pyrimidin-2-yl)cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide(Non-covalent)

J6D.1: 29 residues within 4Å: Chain A: F.194, P.198, R.201, L.205, L.315, V.316, C.317, D.320, L.321, V.322, L.361, I.364, S.366, C.367, S.369, N.370, V.371, L.385, I.414, Q.415, Y.416, F.446, M.448, Y.449, Y.453, L.467, W.551, F.552, A.556 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.194, A:P.198, A:L.205, A:L.205, A:V.322, A:L.385, A:L.385, A:F.446, A:L.467 Hydrogen bonds: A:S.366, A:S.366, A:Q.415 Water bridges: A:R.201, A:R.201, A:Y.453 pi-Stacking: A:Y.453

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 5 residues within 4Å: Chain A: S.6, W.7, T.8, G.276, Y.277 No protein-ligand interaction detected (PLIP) SCN.3: 6 residues within 4Å: Chain A: R.387, T.391, P.392, R.395, S.408, N.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.395, A:S.408, A:N.412 Water bridges: A:A.396 SCN.4: 2 residues within 4Å: Chain A: R.82, L.92 No protein-ligand interaction detected (PLIP)

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.5: 11 residues within 4Å: Chain A: K.101, Y.102, P.136, T.137, T.138, D.165, F.268, N.269, S.270, K.271, G.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.101, A:Y.102 Water bridges: A:T.138

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: Y.34, T.400, H.429, P.496, W.501, R.504 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.34, A:T.400, A:T.400, A:R.504 Water bridges: A:R.33 GOL.7: 7 residues within 4Å: Chain A: S.97, A.98, Y.163, R.169, G.284, G.450, D.560 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.98, A:G.284, A:G.450 Water bridges: A:D.560, A:D.560 GOL.8: 4 residues within 4Å: Chain A: W.7, A.10, S.47, A.50 3 PLIP interactions: 3 interactions with chain A Water bridges: A:I.12, A:S.47, A:S.47 GOL.9: 5 residues within 4Å: Chain A: D.214, S.327, G.329, T.330, Y.359 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.214 Water bridges: A:D.214, A:D.214, A:S.327 GOL.10: 5 residues within 4Å: Chain A: S.191, Y.297, P.312, T.313, M.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.191, A:Y.297, A:Y.297 Water bridges: A:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeung, K.S. et al., Structure-Property Basis for Solving Transporter-Mediated Efflux and Pan-Genotypic Inhibition in HCV NS5B Inhibitors. ACS Med Chem Lett (2018)

Release Date

2018-11-21

Peptides

RNA-dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-dependent RNA polymerase

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