SMTL ID : 6h9r.1

Dengue-RdRp3-inhibitor complex soaking

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x 5V5: 2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid(Non-covalent)

5V5.1: 11 residues within 4Å: Chain A: L.246, C.444, H.446, R.464, M.496, Y.501, T.529, S.531, H.533, A.534, W.538 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.246, A:W.538 Hydrogen bonds: A:S.531 Water bridges: A:W.530, A:W.530

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: E.172, H.176, C.181, G.182, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.172, A:H.176, A:C.181, A:C.184 ZN.3: 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

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

PEG.4: 1 residues within 4Å: Chain A: D.561 No protein-ligand interaction detected (PLIP) PEG.5: 3 residues within 4Å: Chain A: N.370, H.372, L.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.370 PEG.6: 2 residues within 4Å: Chain A: P.557, W.558 No protein-ligand interaction detected (PLIP) PEG.7: 3 residues within 4Å: Chain A: P.260, R.389, R.392 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.389, A:R.389, A:R.392 PEG.8: 5 residues within 4Å: Chain A: Q.440, S.445, H.446, H.447, P.465 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.440, A:S.445 PEG.9: 4 residues within 4Å: Chain A: W.114, R.117, R.121, E.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.117, A:E.383 PEG.10: 3 residues within 4Å: Chain A: Y.238, V.387, K.391 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.391 PEG.11: 3 residues within 4Å: Chain A: L.483, R.484, I.609 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.483, A:I.609

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Riccio, F. et al., Development and validation of RdRp Screen, a crystallization screen for viral RNA-dependent RNA polymerases. Biol Open (2019)

Release Date

2019-03-13

Peptides

Genome polyprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Genome polyprotein

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