SMTL ID : 5pzn.2 (1 other biounit)

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(TERT-BUTYLCARBAMOYL)PHENYL]-2-(4-FLUOROPHENYL)-N-METHYL-1-BENZOFURAN-3-CARBOXAMIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x 23E: (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid(Non-covalent)

23E.1: 19 residues within 4Å: Chain A: L.393, A.394, A.396, A.397, T.400, I.425, L.426, H.429, F.430, L.493, G.494, V.495, P.496, P.497, R.499, V.500, W.501, R.504 Ligands: GOL.11 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.393, A:A.396, A:A.397, A:I.425, A:F.430, A:L.493, A:V.495, A:P.496, A:P.496, A:V.500, A:W.501, A:W.501 Hydrogen bonds: A:R.504, A:R.504 Salt bridges: A:R.499

1 x 8XP: 5-[3-(tert-butylcarbamoyl)phenyl]-2-(4-fluorophenyl)-N-methyl-1-benzofuran-3-carboxamide(Non-covalent)

8XP.2: 25 residues within 4Å: Chain A: F.194, 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, I.414, M.415, I.448, Y.449, Y.453, L.467, W.551, F.552 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.194, A:L.205, A:V.322, A:I.448, A:Y.449, A:Y.449, A:Y.449, A:Y.449, A:Y.453 Hydrogen bonds: A:R.201, A:S.366, A:S.366 Water bridges: A:R.201 pi-Cation interactions: A:R.201

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

SO4.3: 2 residues within 4Å: Chain A: G.517, R.518 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.518 Salt bridges: A:R.518 SO4.4: 2 residues within 4Å: Chain A: K.380, R.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.381 Salt bridges: A:R.381 SO4.5: 2 residues within 4Å: Chain A: H.476, S.477 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.476, A:S.477 Water bridges: A:Y.478, A:Y.478 SO4.6: 5 residues within 4Å: Chain A: R.49, K.52, T.222, R.223, C.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:C.224 Salt bridges: A:K.52 SO4.7: 5 residues within 4Å: Chain A: F.146, S.368, R.387, T.391, R.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.368, A:T.391 Water bridges: A:T.391 Salt bridges: A:R.387 SO4.8: 5 residues within 4Å: Chain A: S.479, P.480, G.481, E.482 Ligands: GOL.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.479, A:G.481, A:E.482

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain A: D.245, L.246, P.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.245 Water bridges: A:D.245 GOL.10: 8 residues within 4Å: Chain A: N.370, S.372, T.386, S.479, G.481, E.482, R.485 Ligands: SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.370, A:S.372, A:S.479, A:E.482 GOL.11: 4 residues within 4Å: Chain A: A.397, W.398, A.401 Ligands: 23E.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.397 GOL.12: 4 residues within 4Å: Chain A: E.129, D.130, T.131, E.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.129, A:T.131, A:E.132, A:E.132, A:E.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeung, K.S. et al., Discovery of a Hepatitis C Virus NS5B Replicase Palm Site Allosteric Inhibitor (BMS-929075) Advanced to Phase 1 Clinical Studies. J. Med. Chem. (2017)

Release Date

2017-05-10

Peptides

RNA-directed RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

RNA-directed RNA polymerase

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