Structure of PDB 5rf2 Chain A Binding Site BS01

Receptor Information

>5rf2 Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: HVB
• InChI: InChI=1S/C3H8N2/c1-2-3(4)5/h2H2,1H3,(H3,4,5)/p+1
• InChIKey: GNFWGDKKNWGGJY-UHFFFAOYSA-O
• SMILES:
  CACTVS 3.385: CCC(N)=[NH2+]
  OpenEye OEToolkits 2.0.6: CCC(=[NH2+])N
• Formula: C3 H9 N2
• Name: 1-azanylpropylideneazanium
• PDB chain: 5rf2 Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rf2 Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
• Resolution: 1.53 Å
• Binding residue (original residue number in PDB): H41 C44
• Binding residue (residue number reindexed from 1): H41 C44
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:5rf2, PDBe:5rf2, PDBj:5rf2
• PDBsum: 5rf2
• PubMed: 33028810
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)