SMTL ID : 5qj1.1

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

1 x J6J: 6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide(Non-covalent)

J6J.1: 24 residues within 4Å: Chain A: F.194, Q.195, Y.196, S.197, P.198, R.201, L.205, L.315, V.316, C.317, D.320, L.321, V.322, I.364, S.366, C.367, S.369, N.370, L.385, Q.415, Y.416, M.448, Y.449, L.467 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.194, A:L.205, A:L.205, A:V.322, A:L.385, A:Q.415, A:Y.416, A:Y.449, A:Y.449, A:L.467 Hydrogen bonds: A:R.201, A:S.366, A:S.366, A:Q.415, A:Y.449 Water bridges: A:R.201, A:Y.416

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

SO4.2: 3 residues within 4Å: Chain A: N.25, S.28, S.31 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.25, A:S.28 Water bridges: A:S.28, A:S.31 SO4.3: 8 residues within 4Å: Chain A: R.423, F.473, S.474, M.475, H.476, N.528, W.529, K.534 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.474 Water bridges: A:R.423, A:H.476, A:K.534 Salt bridges: A:R.423, A:H.476, A:K.534 SO4.4: 4 residues within 4Å: Chain A: R.506, V.531, K.532, T.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.532, A:T.533 Salt bridges: A:R.506 SO4.5: 4 residues within 4Å: Chain A: P.94, S.97, R.169, K.173 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.97 Water bridges: A:T.93, A:A.98, A:K.173 Salt bridges: A:R.169, A:K.173 SO4.6: 2 residues within 4Å: Chain A: Q.273, T.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.274, A:T.274 Water bridges: A:T.274 SO4.7: 6 residues within 4Å: Chain A: G.376, P.377, R.378, G.379, R.380, R.382 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.376, A:R.378, A:R.380 Water bridges: A:R.378, A:R.378 Salt bridges: A:R.378, A:R.380, A:R.382 SO4.8: 5 residues within 4Å: Chain A: E.362, S.372, V.373, S.479, H.481 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.373, A:S.479, A:S.479 Water bridges: A:N.370, A:E.482 SO4.9: 7 residues within 4Å: Chain A: P.95, H.96, R.99, G.105, A.106, K.107, E.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.95, A:R.99, A:A.106, A:K.107 SO4.10: 3 residues within 4Å: Chain A: M.188, G.189, A.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.190 SO4.11: 4 residues within 4Å: Chain A: R.509, I.513, R.524, L.535 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.509, A:R.524 SO4.12: 3 residues within 4Å: Chain A: P.497, L.498, R.499 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.499 Water bridges: A:L.498, A:L.498 Salt bridges: A:R.499

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: Y.5, R.49, V.53, R.159, L.160, D.226, S.227 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.49, A:R.159, A:L.160, A:S.227 Water bridges: A:R.49, A:D.226, A:D.226, A:D.226, A:D.226, A:S.283 GOL.14: 3 residues within 4Å: Chain A: P.247, E.248, E.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.248, A:E.248, A:E.249 GOL.15: 3 residues within 4Å: Chain A: E.465, G.469, L.470 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.465, A:E.465, A:L.470 Water bridges: A:D.471

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

PG4.16: 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 PG4.17: 6 residues within 4Å: Chain A: F.146, C.147, S.368, R.387, T.391, R.395 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.147, A:C.147, A:S.368, A:R.387, A:R.387, A:T.391 PG4.18: 4 residues within 4Å: Chain A: Y.102, H.119, S.122, D.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.122

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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