Structure of PDB 8dif Chain A Binding Site BS01

Receptor Information

>8dif Chain A (length=292) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DCVSFCYMHHMELPGVHAGTDLEGNFGPFVDRQTAQAAGTDTTITVNVLA
WLYAAVINGDRWFLNTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTG
IAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: U1R
• InChI: InChI=1S/C17H12BrNO2/c18-15-8-17(16(10-20)19-9-15)21-11-12-5-6-13-3-1-2-4-14(13)7-12/h1-10H,11H2
• InChIKey: ISBGRJXSCWCLKR-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=Cc1ncc(Br)cc1OCc1cc2ccccc2cc1
  OpenEye OEToolkits 2.0.7: c1ccc2cc(ccc2c1)COc3cc(cnc3C=O)Br
  CACTVS 3.385: Brc1cnc(C=O)c(OCc2ccc3ccccc3c2)c1
• Formula: C17 H12 Br N O2
• Name: 5-bromo-3-[(naphthalen-2-yl)methoxy]pyridine-2-carbaldehyde
• PDB chain: 8dif Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dif Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors.
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): H41 N142 G143 C145 M165 R188 Q189
• Binding residue (residue number reindexed from 1): H41 N140 G141 C143 M161 R182 Q183
• 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:8dif, PDBe:8dif, PDBj:8dif
• PDBsum: 8dif
• PubMed: 37354015
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)