SMTL ID : 3q0z.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-dimer

Ligands

2 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, T.400, I.425, 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:T.400, A:I.425, A:F.430, A:L.493, A:V.495, A:P.496, A:P.497, A:V.500, A:W.501 Hydrogen bonds: A:R.504, A:R.504 Salt bridges: A:R.499 23E.7: 16 residues within 4Å: Chain B: L.393, A.394, A.396, A.397, I.425, H.429, F.430, L.493, G.494, V.495, P.496, P.497, R.499, V.500, W.501, R.504 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.393, B:A.396, B:A.397, B:I.425, B:F.430, B:L.493, B:V.495, B:P.496, B:W.501 Hydrogen bonds: B:R.504, B:R.504 Salt bridges: B:R.499

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

SO4.2: 3 residues within 4Å: Chain A: S.85, V.86, R.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.86 Salt bridges: A:R.121 SO4.3: 5 residues within 4Å: Chain A: R.49, K.52, T.222, R.223, C.224 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.49, A:T.222, A:C.224 Water bridges: A:R.49, A:F.225, A:F.225, A:D.319 Salt bridges: A:K.52 SO4.4: 2 residues within 4Å: Chain A: G.517, R.518 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.518 Water bridges: A:G.516, A:A.519 Salt bridges: A:R.518 SO4.5: 3 residues within 4Å: Chain A: P.497, L.498, R.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.499 Salt bridges: A:R.499 SO4.6: 4 residues within 4Å: Chain A: E.362, S.372, S.479, G.481 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.479, A:S.479, A:G.481 Water bridges: A:N.370, A:E.482 SO4.8: 3 residues within 4Å: Chain B: S.85, V.86, R.121 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.86 Water bridges: B:L.84, B:E.87 Salt bridges: B:R.121 SO4.9: 5 residues within 4Å: Chain B: R.49, K.52, T.222, R.223, C.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.49, B:C.224 Salt bridges: B:K.52 SO4.10: 2 residues within 4Å: Chain B: G.517, R.518 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.518 Water bridges: B:A.519 Salt bridges: B:R.518 SO4.11: 3 residues within 4Å: Chain A: S.2 Chain B: K.380, R.381 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.381, A:S.2 Salt bridges: B:R.381 SO4.12: 2 residues within 4Å: Chain B: H.476, S.477 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.477, B:S.477 Water bridges: B:S.477, B:Y.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, X. et al., Syntheses and initial evaluation of a series of indolo-fused heterocyclic inhibitors of the polymerase enzyme (NS5B) of the hepatitis C virus. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-04-27

Peptides

RNA-directed RNA polymerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

RNA-directed RNA polymerase

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