SMTL ID : 6izx.1

The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: E.228, H.232, C.237, E.238, C.240 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.228, A:H.232, A:C.237, A:C.240 ZN.2: 2 residues within 4Å: Chain A: H.504, C.518 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.518

9 x CO: COBALT (II) ION(Non-covalent)

CO.3: 3 residues within 4Å: Chain A: T.396, G.398, T.401 No protein-ligand interaction detected (PLIP) CO.4: 3 residues within 4Å: Chain A: H.78, T.80, S.81 No protein-ligand interaction detected (PLIP) CO.5: 2 residues within 4Å: Chain A: K.338, R.386 No protein-ligand interaction detected (PLIP) CO.6: 1 residues within 4Å: Chain A: R.444 No protein-ligand interaction detected (PLIP) CO.7: 2 residues within 4Å: Chain A: G.327, K.479 No protein-ligand interaction detected (PLIP) CO.8: 1 residues within 4Å: Chain A: T.101 No protein-ligand interaction detected (PLIP) CO.9: 1 residues within 4Å: Chain A: W.593 No protein-ligand interaction detected (PLIP) CO.10: 1 residues within 4Å: Chain A: W.613 No protein-ligand interaction detected (PLIP) CO.11: 1 residues within 4Å: Chain A: G.349 No protein-ligand interaction detected (PLIP)

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

B5C.12: 6 residues within 4Å: Chain A: V.297, G.299, E.300, G.301, S.451, C.499 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.300, A:G.301 B5C.13: 11 residues within 4Å: Chain A: Q.550, S.553, R.563, N.567, C.570, E.597, D.598, M.599, W.623, Y.672, M.673 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.563, A:M.599, A:W.623 Hydrogen bonds: A:N.567, A:M.599 pi-Stacking: A:Y.672

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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