Structure of PDB 8fy7 Chain B Binding Site BS01

Receptor Information

>8fy7 Chain B (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: YFK
• InChI: InChI=1S/C24H32N4O4/c1-5-16(12-15-9-10-25-22(15)29)26-23(30)19(11-14(2)3)28-24(31)20-13-17-18(27-20)7-6-8-21(17)32-4/h5-8,13-16,19,27H,1,9-12H2,2-4H3,(H,25,29)(H,26,30)(H,28,31)/t15-,16+,19-/m0/s1
• InChIKey: UWAHXCKRRCFZCB-FCEWJHQRSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C=C)NC(=O)c2cc3c([nH]2)cccc3OC
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C=C
  ACDLabs 12.01: COc1cccc2[NH]c(cc12)C(=O)NC(CC(C)C)C(=O)NC(CC1CCNC1=O)C=C
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C=C)NC(=O)c2cc3c([nH]2)cccc3OC
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)C=C
• Formula: C24 H32 N4 O4
• Name: 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)-1-[(3S)-2-oxopyrrolidin-3-yl]but-3-en-2-yl}amino)pentan-2-yl]-1H-indole-2-carboxamide
• PDB chain: 8fy7 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fy7 Alkyne as a Latent Warhead to Covalently Target SARS-CoV-2 Main Protease.
• Resolution: 1.94 Å
• Binding residue (original residue number in PDB): F140 L141 N142 C145 H164 M165 E166 R188 Q189 T190 A191
• Binding residue (residue number reindexed from 1): F140 L141 N142 C145 H164 M165 E166 R188 Q189 T190 A191
• 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:8fy7, PDBe:8fy7, PDBj:8fy7
• PDBsum: 8fy7
• PubMed: 37595260
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)