SMTL ID : 6izz.1

The RNA-dependent RNA polymerase domain of dengue 3 NS5, bound with RK-0404678

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.188, H.192, C.197, G.198, C.200 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.188, A:H.192, A:C.197, A:C.200 ZN.2: 4 residues within 4Å: Chain A: H.463, H.465, C.479, C.598 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.463, A:H.465, A:C.479, A:C.598

1 x B5C: 2-oxo-2H-1,3-benzoxathiol-5-yl acetate(Non-covalent)

B5C.3: 8 residues within 4Å: Chain A: K.507, Q.511, C.531, D.559, M.560, L.561, W.584, Y.633 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.560, A:L.561, A:Y.633, A:Y.633 Hydrogen bonds: A:K.507

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, H. et al., Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase. Plos Negl Trop Dis (2019)

Release Date

2019-12-25

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein

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