SMTL ID : 3hkw.1 (2 other biounits)

HCV NS5B genotype 1a in complex with 1,5 benzodiazepine inhibitor 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x IX6: (11S)-10-[(2,5-dimethyl-1,3-oxazol-4-yl)carbonyl]-11-{2-fluoro-4-[(2-methylprop-2-en-1-yl)oxy]phenyl}-3,3-dimethyl-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide(Non-covalent)

IX6.1: 18 residues within 4Å: Chain A: F.196, P.200, R.203, C.369, S.370, S.371, L.387, R.389, S.410, G.413, N.414, M.417, F.418, E.449, I.450, Y.451, G.452, S.559 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.387, A:L.387, A:F.418, A:Y.451, A:Y.451 Hydrogen bonds: A:S.370, A:S.370, A:R.389, A:S.559 Water bridges: A:S.370, A:R.389, A:S.559

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

SO4.2: 3 residues within 4Å: Chain A: N.27, L.29, R.439 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.27, A:N.27 Salt bridges: A:R.439 SO4.3: 3 residues within 4Å: Chain A: K.212, R.383, Y.385 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.385 Water bridges: A:Y.385, A:Y.385 Salt bridges: A:K.212, A:R.383 SO4.4: 2 residues within 4Å: Chain A: R.35, H.36 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.35, A:H.36 SO4.5: 4 residues within 4Å: Chain A: R.508, V.533, R.534, T.535 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.504, A:R.534, A:T.535, A:T.535 Water bridges: A:R.508, A:R.508 Salt bridges: A:R.508 SO4.6: 4 residues within 4Å: Chain A: E.443, L.460, G.519, R.520 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.520 Water bridges: A:E.443, A:G.518 Salt bridges: A:R.520 SO4.7: 5 residues within 4Å: Chain A: R.51, K.54, T.224, R.225, C.226 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.51, A:T.224, A:C.226 Water bridges: A:F.227, A:F.227 Salt bridges: A:K.54 SO4.10: 2 residues within 4Å: Chain A: H.478, S.479 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.479 Water bridges: A:Y.480 Salt bridges: A:H.478

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: I.26, N.31, R.35, H.37 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.31, A:N.31 Water bridges: A:H.37 GOL.9: 5 residues within 4Å: Chain A: S.32, P.498, A.502, W.503, R.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.502 GOL.11: 3 residues within 4Å: Chain A: Q.61, L.63, S.234 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.61, A:S.234, A:S.234 Water bridges: A:L.63, A:S.234, A:T.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nyanguile, O. et al., 1a/1b subtype profiling of nonnucleoside polymerase inhibitors of hepatitis C virus. J.Virol. (2010)

Release Date

2010-05-26

Peptides

NS5B RNA-dependent RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS5B RNA-dependent RNA polymerase

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