SMTL ID : 5czb.1 (1 other biounit)

HCV NS5B IN COMPLEX WITH LIGAND IDX17119-5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x 55W: 1-[4-(7-amino-5-methylpyrazolo[1,5-a]pyrimidin-2-yl)phenyl]-3-{[(R)-(2,4-dimethylphenyl)(methoxy)phosphoryl]amino}-1H-pyrazole-4-carboxylic acid(Non-covalent)

55W.1: 19 residues within 4Å: Chain A: L.420, R.423, M.424, L.475, H.476, S.477, Y.478, I.483, A.487, L.490, R.491, V.495, P.496, P.497, L.498, W.501, R.502, W.529, K.534 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.420, A:L.420, A:R.423, A:H.476, A:I.483, A:A.487, A:L.498, A:L.498, A:L.498, A:W.529, A:W.529, A:W.529 Hydrogen bonds: A:S.477, A:Y.478, A:P.496, A:R.502 Water bridges: A:L.498, A:L.498

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.97, A.98, K.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.99 GOL.3: 3 residues within 4Å: Chain A: T.500, H.503, R.504 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.503, A:R.504

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 3 residues within 4Å: Chain A: L.498, R.499, R.502 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.499, A:R.502

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 5 residues within 4Å: Chain A: L.84, S.85, R.121, W.124, M.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.84 PEG.6: 4 residues within 4Å: Chain A: L.128, P.248, E.249, Q.252 No protein-ligand interaction detected (PLIP) PEG.7: 4 residues within 4Å: Chain A: E.465, G.469, L.470, S.471 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.470, A:S.471 Water bridges: A:E.465, A:G.469 PEG.8: 6 residues within 4Å: Chain A: S.97, A.98, F.163, R.169, G.284, G.558 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.97, A:A.98

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

SO4.9: 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 SO4.10: 2 residues within 4Å: Chain A: R.499, R.506 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.506 Salt bridges: A:R.499, A:R.506 SO4.11: 2 residues within 4Å: Chain A: S.113, S.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.114 Water bridges: A:S.113, A:R.115 SO4.12: 5 residues within 4Å: Chain A: R.49, K.52, T.222, R.223, C.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.224 Water bridges: A:F.225, A:F.225 Salt bridges: A:R.49, A:K.52 SO4.13: 1 residues within 4Å: Chain A: R.115 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.115 SO4.14: 2 residues within 4Å: Chain A: H.503, R.506 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.506 Salt bridges: A:H.503, A:R.506 SO4.15: 1 residues within 4Å: Chain A: R.499 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.499, A:R.499, A:R.499, A:R.499, A:R.499 Salt bridges: A:R.499 SO4.16: 6 residues within 4Å: Chain A: T.288, S.289, N.292, G.318, D.319, S.557 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.288, A:N.292, A:D.319, A:S.557 SO4.17: 4 residues within 4Å: Chain A: R.33, H.34, H.35, N.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.34, A:N.36, A:N.36 Salt bridges: A:H.35 SO4.18: 2 residues within 4Å: Chain A: K.80, D.245 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pierra Rouviere, C. et al., Synthesis of potent and broad genotypically active NS5B HCV non-nucleoside inhibitors binding to the thumb domain allosteric site 2 of the viral polymerase. Bioorg.Med.Chem.Lett. (2016)

Release Date

2016-06-15

Peptides

NS5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NS5B

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