SMTL ID : 8xko.1

CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

1 x 01: [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

01.1: 17 residues within 4Å: Chain A: K.547, K.553, R.555, R.557, D.620, K.623, C.624, S.684, T.689, N.693, K.800 Chain E: G.14 Chain F: U.5, C.6 Ligands: MG.2, MG.3, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.547, A:K.623, A:C.624 Salt bridges: A:K.553, A:K.553, A:K.553, A:R.555, A:K.623 Halogen bonds: A:T.689

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.620, K.800 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.620 MG.3: 2 residues within 4Å: Chain A: K.553 Ligands: 01.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: S.551, R.555 Ligands: 01.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode. To Be Published

Release Date

2024-12-04

Peptides

RNA-directed RNA polymerase nsp12: 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 nsp12

Non-structural protein 8

Non-structural protein 7

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