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

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE C316N IN COMPLEX WITH 2-(4-FLUOROPHENYL)-N-METHYL-5-[3-({2-METHYL-1-OXO-1-[(1,3,4-THIADIAZOL-2-YL)AMINO]PROPAN-2-YL}CARBAMOYL)PHENYL]-1-BENZOFURAN-3-CARBOXAMIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.393, A:A.396, A:A.397, A:I.425, A:L.426, A:F.430, A:L.493, A:V.495, A:P.496, A:P.496, A:V.500, A:W.501 Hydrogen bonds: A:R.504, A:R.504 Salt bridges: A:R.499

1 x 8XM: 2-(4-fluorophenyl)-N-methyl-5-[3-({2-methyl-1-oxo-1-[(1,3,4-thiadiazol-2-yl)amino]propan-2-yl}carbamoyl)phenyl]-1-benzofuran-3-carboxamide(Non-covalent)

8XM.2: 26 residues within 4Å: Chain A: F.194, Q.195, Y.196, S.197, P.198, R.201, L.205, L.315, N.317, D.320, L.321, V.322, I.364, T.365, S.366, C.367, S.369, N.370, L.385, I.414, M.415, Y.416, I.448, Y.449, Y.453, L.467 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.205, A:V.322, A:L.385, A:I.448, A:Y.449, A:Y.449, A:Y.453 Hydrogen bonds: A:R.201, A:S.366, A:S.366, A:S.369 Water bridges: A:Y.196, A:R.201, A:R.201 pi-Stacking: A:Y.449

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

SO4.3: 3 residues within 4Å: Chain A: E.441, G.517, R.518 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.441, A:R.518 Salt bridges: A:R.518 SO4.4: 2 residues within 4Å: Chain A: K.380, R.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.381 Salt bridges: A:K.380, A:R.381 SO4.5: 2 residues within 4Å: Chain A: H.476, S.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.476, A:S.477 SO4.6: 3 residues within 4Å: Chain A: S.479, P.480, G.481 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.479, A:S.479, A:G.481, A:E.482

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: K.80, D.245 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.245 GOL.8: 5 residues within 4Å: Chain A: D.245, L.246, P.248, R.251 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.245, A:L.246, A:R.251 GOL.9: 3 residues within 4Å: Chain A: A.397, A.401 Ligands: 23E.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.397 GOL.10: 4 residues within 4Å: Chain A: S.368, R.387, T.391, R.395 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.368, A:R.387, A:T.391, A:T.391, A:R.395, A:R.395

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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