Structure of PDB 6xb1 Chain A Binding Site BS01

Receptor Information

>6xb1 Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: NEN
• InChI: InChI=1S/C6H9NO2/c1-2-7-5(8)3-4-6(7)9/h2-4H2,1H3
• InChIKey: GHAZCVNUKKZTLG-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341
  OpenEye OEToolkits 1.5.0: CCN1C(=O)CCC1=O
  ACDLabs 10.04: O=C1N(C(=O)CC1)CC
• Formula: C6 H9 N O2
• Name: 1-ETHYL-PYRROLIDINE-2,5-DIONE
• DrugBank: DB01902
• ZINC: ZINC000001670837
• PDB chain: 6xb1 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xb1 Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro : insights into enzyme mechanism and drug design.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): K102 C156
• Binding residue (residue number reindexed from 1): K102 C156
• 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:6xb1, PDBe:6xb1, PDBj:6xb1
• PDBsum: 6xb1
• PubMed: 33063790
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)