SMTL ID : 5jjs.1

Dengue 3 NS5 protein with compound 27

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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

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

PEG.3: 6 residues within 4Å: Chain A: C.390, T.391, R.435, Y.479, E.483, L.560 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.390 Water bridges: A:R.392, A:Y.479 PEG.6: 10 residues within 4Å: Chain A: G.90, Y.116, D.253, L.254, G.255, K.297, K.352, E.353, D.356, T.357 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.253, A:K.352 Water bridges: A:G.90, A:Y.116, A:D.356 PEG.12: 7 residues within 4Å: Chain A: V.63, E.64, P.295, Q.348, R.349, K.352 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.63 Hydrogen bonds: A:E.64, A:E.64 Water bridges: A:Y.87, A:K.352 PEG.15: 4 residues within 4Å: Chain A: I.871, G.872, N.873, E.874 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.873, A:E.874

1 x 6L2: 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-{[(1R,3R)-3-methoxycyclohexyl]sulfonyl}benzamide(Non-covalent)

6L2.4: 18 residues within 4Å: Chain A: L.508, H.509, C.706, S.707, H.708, R.726, R.734, M.758, M.762, Y.763, T.791, W.792, S.793, H.795, A.796, H.797, Q.799, W.800 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.508, A:L.508, A:W.792, A:W.800 Hydrogen bonds: A:H.509, A:R.726, A:R.726, A:T.791, A:W.792, A:S.793, A:H.797, A:H.797, A:Q.799 Water bridges: A:S.707, A:R.734

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: A.528, D.530, D.661, C.662 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.530, A:D.661, H2O.5, H2O.6, H2O.9, H2O.10

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

EDO.7: 6 residues within 4Å: Chain A: K.11, L.14, N.15, S.147, S.148, P.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.15 Water bridges: A:K.11, A:K.11 EDO.8: 3 residues within 4Å: Chain A: R.54, K.58, L.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.54 Water bridges: A:K.58, A:E.213 EDO.10: 2 residues within 4Å: Chain A: R.496, K.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.496, A:K.653 EDO.11: 3 residues within 4Å: Chain A: E.4, E.8, K.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.12, A:K.12 EDO.13: 7 residues within 4Å: Chain A: E.64, N.66, E.293, P.295, Q.348, R.578 Ligands: PEG.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.66, A:E.293, A:R.578 EDO.14: 3 residues within 4Å: Chain A: K.627, L.676, W.691 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.627 EDO.16: 6 residues within 4Å: Chain A: K.398, F.482, G.486, N.489, E.490, V.600 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.490, A:E.490 Water bridges: A:N.489, A:N.489, A:G.601 EDO.17: 7 residues within 4Å: Chain A: P.704, S.707, H.708, H.709, C.725, R.726, P.727 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.709, A:C.725 Water bridges: A:E.730 EDO.18: 5 residues within 4Å: Chain A: Q.702, H.709, H.711, W.843, C.844 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.711

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

SAH.9: 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:D.128, A:D.128, A:V.129 Water bridges: A:R.81, A:S.85, A:R.160, A:R.160 pi-Stacking: A:H.107

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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