SMTL ID : 3qgf.1 (1 other biounit)

Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase complex with (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 and (2R)-4-(6-chloropyridazin-3-yl)-N-(4-methoxybenzyl)-1-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazine-2-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 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: 17 residues within 4Å: Chain A: L.393, A.394, A.396, A.397, 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 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:L.493, A:V.495, A:P.497, A:V.500, A:W.501 Hydrogen bonds: A:R.504, A:R.504 Salt bridges: A:R.499

1 x 46F: (2R)-4-(6-chloropyridazin-3-yl)-N-(4-methoxybenzyl)-1-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazine-2-carboxamide(Non-covalent)

46F.2: 22 residues within 4Å: Chain A: Y.192, G.193, F.194, Y.196, S.197, P.198, R.201, S.289, C.367, S.369, M.415, I.448, Y.449, A.451, Y.453, I.455, I.463, L.467, L.548, W.551, Y.556, S.557 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.194, A:I.448, A:Y.449, A:Y.449, A:Y.453, A:Y.453, A:L.467, A:L.467, A:L.548, A:L.548 Hydrogen bonds: A:Y.196

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

SO4.3: 4 residues within 4Å: Chain A: S.85, V.86, E.87, R.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.86 Salt bridges: A:R.121 SO4.4: 4 residues within 4Å: Chain A: R.49, K.52, R.223, C.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.222, A:C.224 Salt bridges: A:R.49, A:K.52 SO4.5: 3 residues within 4Å: Chain A: L.458, G.517, R.518 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.518 Water bridges: A:G.516, A:R.518, A:R.518, A:A.519 Salt bridges: A:R.518 SO4.6: 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 SO4.7: 4 residues within 4Å: Chain A: R.506, V.531, R.532, T.533 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.532, A:T.533, A:T.533 Salt bridges: A:R.506, A:R.532 SO4.8: 4 residues within 4Å: Chain A: R.502, H.503, R.506, R.532 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.503, A:R.506, A:R.532

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gentles, R.G. et al., Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-04-20

Peptides

RNA-directed RNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-directed RNA polymerase

Related Entries With Identical Sequence