SMTL ID : 7ctt.1

Cryo-EM structure of Favipiravir bound to replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310 ZN.2: 4 residues within 4Å: Chain A: C.487, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: W.617, D.761, W.800, E.811 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.761

1 x GE6: [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

GE6.4: 16 residues within 4Å: Chain A: K.545, R.553, R.555, V.557, D.618, K.621, C.622, D.623, S.682, T.687, N.691, D.760, K.798 Chain E: A.20 Chain F: C.20, U.21 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.621, A:C.622, A:D.623, A:D.623, A:D.623, A:S.682, A:N.691, A:D.760 Salt bridges: A:R.553, A:R.553, A:R.555, A:K.621, A:K.798, A:K.798, A:K.798 pi-Cation interactions: A:R.555

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, Q. et al., Structural Basis of SARS-CoV-2 Polymerase Inhibition by Favipiravir. Innovation (N Y) (2021)

Release Date

2020-09-02

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

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