SMTL ID : 5hmz.1

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.447, H.449, C.463, C.582 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.447, A:H.449, A:C.463, A:C.582 ZN.2: 4 residues within 4Å: Chain A: E.172, H.176, C.181, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.172, A:H.176, A:C.181, A:C.184

1 x LNZ: 5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-4-methoxy-2-methyl-N-(methylsulfonyl)benzamide(Non-covalent)

LNZ.3: 19 residues within 4Å: Chain A: L.246, H.247, C.444, S.445, H.446, R.464, R.472, M.496, M.500, Y.501, T.528, T.529, W.530, S.531, H.533, A.534, H.535, Q.537, W.538 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.246, A:L.246, A:T.529, A:A.534, A:W.538 Hydrogen bonds: A:H.247, A:R.464, A:R.464, A:T.529, A:W.530, A:S.531, A:H.535, A:Q.537, A:Q.537 Water bridges: A:R.472

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokokawa, F. et al., Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design. J.Med.Chem. (2016)

Release Date

2016-03-30

Peptides

RNA-directed RNA polymerase NS5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA-directed RNA polymerase NS5

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