SMTL ID : 5jjr.1

Dengue 3 NS5 protein with compound 29

Coordinates

PDB Format

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: E.434, H.438, C.443, C.446 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.434, A:H.438, A:C.443, A:C.446 ZN.2: 4 residues within 4Å: Chain A: H.709, H.711, C.725, C.844 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.709, A:H.711, A:C.725, A:C.844

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.3: 18 residues within 4Å: Chain A: S.53, G.55, G.78, C.79, G.80, G.82, G.83, W.84, T.101, K.102, H.107, E.108, K.127, D.128, V.129, F.130, D.143, I.144 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.53, A:G.82, A:G.83, A:W.84, A:W.84, A:W.84, A:K.102, A:H.107, A:E.108, A:E.108, A:E.108, A:D.128, A:V.129, A:D.143 Water bridges: A:S.85, A:D.143 pi-Stacking: A:H.107

1 x 68E: 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-4-methoxy-2-methyl-N-[(quinolin-8-yl)sulfonyl]benzamide(Non-covalent)

68E.4: 19 residues within 4Å: Chain A: M.337, L.508, H.509, C.706, S.707, H.708, R.726, R.734, M.758, M.762, Y.763, T.791, S.793, H.795, A.796, H.797, H.798, Q.799, W.800 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.508, A:L.508, A:T.791, A:W.800 Hydrogen bonds: A:R.726, A:R.726, A:S.793, A:H.797, A:H.797, A:H.798, A:Q.799 Water bridges: A:W.792

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: K.11, L.14, N.15, S.147, S.148, P.149 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.15 EDO.7: 2 residues within 4Å: Chain A: N.489, I.794 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.601 Water bridges: A:G.604 EDO.9: 4 residues within 4Å: Chain A: N.449, W.474, G.598 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.449 EDO.11: 4 residues within 4Å: Chain A: R.496, D.517, I.518, K.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.496 Water bridges: A:D.517 EDO.12: 6 residues within 4Å: Chain A: V.63, N.66, I.69, E.293, P.295 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.293 Water bridges: A:N.66, A:N.66 EDO.13: 7 residues within 4Å: Chain A: I.69, K.92, K.93, E.293, N.294, P.295 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.93, A:K.93 Water bridges: A:K.92

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 5 residues within 4Å: Chain A: A.528, D.530, D.661, C.662, P.704 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.530, A:D.661, H2O.2, H2O.2, H2O.5, H2O.7

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

PEG.8: 5 residues within 4Å: Chain A: K.398, W.474, R.478, V.600 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.398, A:K.398 PEG.10: 7 residues within 4Å: Chain A: G.29, I.30, T.31, R.203, P.205, L.234, R.238 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.205, A:R.238, A:R.238 Water bridges: A:T.31, A:R.203, A:R.203 PEG.14: 8 residues within 4Å: Chain A: E.32, V.33, D.34, R.35, T.36, K.39, R.54, I.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.32, A:R.35, A:K.39, A:R.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lim, S.P. et al., Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling. Plos Pathog. (2016)

Release Date

2016-07-06

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein

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