Structure of PDB 5rfy Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: T8S
• InChI: InChI=1S/C12H22N2O2/c1-9(2)13(4)12(16)11-5-7-14(8-6-11)10(3)15/h9,11H,5-8H2,1-4H3
• InChIKey: CELKOAKJTFSHIV-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(C)N(C)C(=O)C1CCN(CC1)C(C)=O
  ACDLabs 12.01: N1(CCC(C(N(C(C)C)C)=O)CC1)C(=O)C
  OpenEye OEToolkits 2.0.7: CC(C)N(C)C(=O)C1CCN(CC1)C(=O)C
• Formula: C12 H22 N2 O2
• Name: 1-acetyl-N-methyl-N-(propan-2-yl)piperidine-4-carboxamide
• PDB chain: 5rfy Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rfy Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G143 C145
• Binding residue (residue number reindexed from 1): G143 C145
• 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:5rfy, PDBe:5rfy, PDBj:5rfy
• PDBsum: 5rfy
• PubMed: 33028810
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)