Structure of PDB 5rfp Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: T7V
• InChI: InChI=1S/C10H12ClNO/c1-7(12-8(2)13)9-4-3-5-10(11)6-9/h3-7H,1-2H3,(H,12,13)/t7-/m0/s1
• InChIKey: XDFGWKFEFHPPQO-ZETCQYMHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C[C@H](c1cccc(c1)Cl)NC(=O)C
  ACDLabs 12.01: c1cc(Cl)cc(C(C)NC(=O)C)c1
  OpenEye OEToolkits 2.0.7: CC(c1cccc(c1)Cl)NC(=O)C
  CACTVS 3.385: C[C@H](NC(C)=O)c1cccc(Cl)c1
  CACTVS 3.385: C[CH](NC(C)=O)c1cccc(Cl)c1
• Formula: C10 H12 Cl N O
• Name: N-[(1S)-1-(3-chlorophenyl)ethyl]acetamide
• PDB chain: 5rfp Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rfp Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
• Resolution: 2.03 Å
• Binding residue (original residue number in PDB): H41 C145 H164 M165 D187 Q189
• Binding residue (residue number reindexed from 1): H41 C145 H164 M165 D187 Q189
• 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:5rfp, PDBe:5rfp, PDBj:5rfp
• PDBsum: 5rfp
• PubMed: 33028810
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)