SMTL ID : 6h80.1

Dengue-RdRp3-inhibitor complex co-crystallisation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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:R.472, A:S.531

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: E.172, C.181, G.182, C.184 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.181, A:C.184 ZN.3: 4 residues within 4Å: Chain A: H.447, H.449, C.463, C.582 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.447, A:H.447, A:H.449, A:C.463, A:C.582

5 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: 2 residues within 4Å: Chain A: N.370, H.372 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: 4 residues within 4Å: Chain A: P.260, R.389, R.392, I.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.389, A:R.392 PEG.8: 4 residues within 4Å: Chain A: Q.440, S.445, H.446, H.447 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.445

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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