SMTL ID : 7ed5.1

A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.98 Å

Oligo State

hetero-1-2-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.319, C.325, C.330, C.334 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.319, A:C.325, A:C.330, A:C.334 ZN.2: 5 residues within 4Å: Chain A: C.511, F.595, H.666, C.669, C.670 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.511, A:H.666, A:C.669, A:C.670

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.233, D.242 Ligands: AT9.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.242 MG.6: 5 residues within 4Å: Chain A: D.642, Y.643, D.784, K.822 Ligands: AT9.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.642, A:D.642 MG.7: 2 residues within 4Å: Chain A: D.242 Ligands: AT9.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.242, A:D.242

3 x AT9: [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

AT9.4: 18 residues within 4Å: Chain A: V.55, R.57, F.59, K.74, C.77, R.79, V.95, K.97, R.140, L.143, T.144, K.145, T.147, D.232, Y.241, D.242 Ligands: MG.3, MG.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.57, A:R.57, A:R.79, A:T.144, A:D.232, A:Y.241 Salt bridges: A:K.74, A:K.97, A:K.97, A:R.140 AT9.5: 15 residues within 4Å: Chain A: K.569, R.577, P.644, K.645, C.646, D.647, S.706, T.711, N.715, D.784, K.822 Chain F: C.9, C.10 Ligands: MG.6, AT9.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.647 Hydrogen bonds: A:K.645, A:C.646, A:S.706, A:N.715 Salt bridges: A:R.577, A:R.577, A:K.645, A:K.822 AT9.8: 10 residues within 4Å: Chain A: L.782, S.783, D.784, D.785, C.837, S.838 Chain E: U.20 Chain F: C.10, A.11 Ligands: AT9.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.784, A:D.784 Halogen bonds: A:S.783

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shannon, A. et al., A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase. Nat Commun (2022)

Release Date

2022-02-16

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 8: BD
Non-structural protein 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7