Structure of PDB 5rep Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: T3G
• InChI: InChI=1S/C12H14F2N2O3S/c1-9(17)15-5-7-16(8-6-15)20(18,19)12-10(13)3-2-4-11(12)14/h2-4H,5-8H2,1H3
• InChIKey: IQKBRWMUAKOXSG-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: N2(CCN(S(c1c(cccc1F)F)(=O)=O)CC2)C(=O)C
  CACTVS 3.385: CC(=O)N1CCN(CC1)[S](=O)(=O)c2c(F)cccc2F
  OpenEye OEToolkits 2.0.7: CC(=O)N1CCN(CC1)S(=O)(=O)c2c(cccc2F)F
• Formula: C12 H14 F2 N2 O3 S
• Name: 1-{4-[(2,6-difluorophenyl)sulfonyl]piperazin-1-yl}ethan-1-one
• PDB chain: 5rep Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rep Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
• Resolution: 1.81 Å
• Binding residue (original residue number in PDB): H41 N142 G143 C145
• Binding residue (residue number reindexed from 1): H41 N142 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:5rep, PDBe:5rep, PDBj:5rep
• PDBsum: 5rep
• PubMed: 33028810
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)