SMTL ID : 5uj2.1

Crystal structure of HCV NS5B genotype 2A JFH-1 isolate with S15G E86Q E87Q C223H V321I mutations and Delta8 neta hairpoin loop deletion in complex with GS-639476 (diphsohate version of GS-9813), Mn2+ and symmetrical primer template 5'-AUAAAUUU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

2 x A- U- A- A- A- U- U- U: RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3')(Non-covalent)

A-U-A-A-A-U-U-U.1: 27 residues within 4Å: Chain A: P.95, S.98, A.99, K.143, I.162, Y.164, R.170, K.174, Q.182, F.195, Y.197, S.198, P.199, S.284, G.285, V.286, L.287, S.290, I.415, I.456, L.460 Ligands: A-A-A-U-U-U.2, A-A-A-U-U-U.2, A-A-A-U-U-U.2, A-A-A-U-U-U.2, A-A-A-U-U-U.2, 8B4.4 Protein-ligand interaction information (PLIP) not available A-U-A-A-A-U-U-U.2: 23 residues within 4Å: Chain A: H.97, C.318, G.319, D.320, D.321, C.368, S.369, R.388, R.396, N.408, S.409, G.412, N.413, Q.416, Y.446 Ligands: A-U-A-A-A-U-U-U.1, A-U-A-A-A-U-U-U.1, A-U-A-A-A-U-U-U.1, A-U-A-A-A-U-U-U.1, A-U-A-A-A-U-U-U.1, A-U-A-A-A-U-U-U.1, MN.3, 8B4.4 Protein-ligand interaction information (PLIP) not available

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 6 residues within 4Å: Chain A: D.222, D.320, D.321 Ligands: A-A-A-U-U-U.2, 8B4.4, MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:D.320, A:D.321, H2O.1 MN.5: 5 residues within 4Å: Chain A: D.222, T.223, D.320 Ligands: MN.3, 8B4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.222, A:T.223, A:D.320, H2O.1 MN.6: 2 residues within 4Å: Chain A: E.239, H.256 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.239, A:H.256

1 x 8B4: (1S)-1-(4-aminoimidazo[2,1-f][1,2,4]triazin-7-yl)-1,4-anhydro-2-deoxy-2-fluoro-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-2-methyl-D-ribitol(Non-covalent)

8B4.4: 18 residues within 4Å: Chain A: R.50, K.143, R.160, I.162, D.222, T.223, H.225, F.226, D.227, S.284, T.289, N.293, D.320 Ligands: A-U-A-A-A-U-U-U.1, A-U-A-A-A-U-U-U.1, A-A-A-U-U-U.2, MN.3, MN.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.50, A:R.160, A:H.225, A:H.225, A:F.226, A:D.227, A:D.227, A:N.293 Salt bridges: A:R.160, A:R.160

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: G.377, P.378, R.379, G.380, R.381 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kirschberg, T.A. et al., Discovery of a 2'-fluoro-2'-C-methyl C-nucleotide HCV polymerase inhibitor and a phosphoramidate prodrug with favorable properties. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-03-22

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein